Doctor Whooves of Equestria
by Kiaooftheblade
Summary: The Doctor, time traveling protector of the universe, finds himself in a strange new world, and is somehow a pony! Join the Doctor as he sets off to explore this strange new world and maybe find his way back home.
1. Brave New World

I don't own My Little Pony or Doctor Who and any related characters in any way, shape, or form.

* * *

Chapter 1 Brave New World

It was a calm day. The sun was high and shining brightly, a soft breeze was blowing, and everything was at peace. The calm was suddenly interrupted by a soft whooshing sound. As the sound continued, a large blue box slowly faded into visibleness. When the box finally became solid and fully visible, the sound abruptly stopped and the door on the front opened.

"Well now, this is a bit odd," a male voice with a slight accent said from within, "This is definitely not London."

Stepping out, the occupant of the box looked at his surroundings, squinting at everything, as if trying to make sense of what he was seeing.

"Looks like Earth," he said, sniffing the air and sticking out his tongue, "Smells like Earth. Even tastes like Earth. But definitely not London. Just where am I?"

Turning, he stepped back into the box and made his way to a large console in the center of the impossibly large room contained within.

"Lets see what the TARDIS has to say," he said to himself.

He began furiously typing away on the keyboard in front of him, as well as pressing various buttons and pulling different levers. Within a few moments, a screen came down from the ceiling and blazed to life.

"All right, where are we then?" the man said as he took a look, "Ponyville, Equestria on planet Earth. Wait, what? I've never heard of a country called Equestria on Earth. Blasted thing must be on the fritz again. I'll fix it later. For now, I'd best take a look around and see where I really am."

Pressing another button, the screen turned off, becoming a dark reflective surface. He was just about to send the screen away when he noticed something odd within the image of his own face being reflected back at him. Namely, the fact that it didn't appear to be him.

"What the…" he said reaching up to touch his face, "How is this even- Why do I have hooves? TARDIS, full body mirror!"

A large mirror rose out of the floor behind him and he turned to look.

"Oh, this is not good…"

The image of himself that he saw was rather surprising. Rather than the two legged, pink-skinned humanoid form he was so accustomed to, what he saw was a horse. A small horse, more like a pony.

"How is this even possible? Can Time Lords really take on forms like this? I've never heard of something like this happening, but then again, there is a lot I don't know…"

He looked over the body, taking in every detail. "Brown coat, brown mane and tail. Will I ever be ginger? Oh, hello. What is that?" On his rump, he noticed an image of an hourglass. "How curious… It doesn't appear to be brand and I don't think horses can be tattooed. It's almost as if each individual hair is a different color. I rather like that it's an hourglass. Seems rather fitting. Doesn't explain why I'm a pony or where I am. Wait, can ponies talk here? Oh I do hope they can. It would be a bit awkward being a talking pony on planet where ponies are silent. Best do some scouting while I try to figure this out."

As he made his way back to the door, the pony suddenly stopped and turned.

"Where's my sonic?" he said looking around, "I'm pretty sure I left it on the console over… There! Found it!" he exclaimed spotting a small metallic cylindrical object sitting on the center console.

He walked over to it and stopped, looking at it for moment before mumbling, "How am I supposed to pick this up? I don't have hands, I have hooves. I can't pick things up with hooves. But then again, I was just typing on the keyboard with hooves. Maybe I can pick it up…"

Reaching out with one of his hooves, the pony tried to grasp the object, but found himself unable to do so. He tried again and again, but each time was unable to actually grab the object.

"Oh blast it all!" he exclaimed turning away, "I knew it was impossible. Guess I'll have to go on without it."

As he walked away, he brushed a hoof along the console and suddenly, the sonic was in his hoof.

"Wait a minute, what?" he looked down at his hoof, very confused by what just happened, "How is this possible? This is a hoof, not a hand! How is it holding my sonic?"

He looked at his hoof for another moment, and then the sonic dropped to the floor. He stared it at for about a minute, then reached down and picked it back up.

"Hmm, well what do you know," he mumbled, "Guess these hooves are like hands. Now I just need a way to carry this… If only I had pockets…"

Placing the sonic back on the console, the pony walked off into another section of the TARDIS and found himself in a large room filled with rows upon rows of clothes. He looked at everything spread out before him and sighed.

"A limitless selection of outfits and none of them made for ponies. There must be something I can wear."

He walked into the massive collection of clothes and started looking through everything for anything that would work with his new form. Then, finally after a few minutes, he found it.

"Well, what do we have here? When did I get a saddlebag?" He picked the bag up and looked it over. "Either way, this should work."

He placed the saddlebag across his back and tightened the various straps, than went back into the main room and grabbed the sonic. Placing it into the saddlebag, he smiled.

"Not quite pockets, but it'll do."

The pony then quickly walked around the TARDIS, gathering up various things and placing them into the saddlebag. With everything finally in order, the pony proceeded back out of the blue box and into the outside world. He found himself in a clearing. There were clumps of trees and bushes all around, as well as a small pond with a small river running away form it. In the distance, the brown pony could see what appeared to be buildings.

"That looks like a good place to go. Should be able to figure something out there."

Making his way towards the apparent town, he began to see other ponies, many of them with brightly colored coats and manes walking about.

"Well now, that is just odd," he said, stopping a little ways outside of the town.

"What's odd?" a cheery voice chirped from beside him.

"All those ponies," he responded, not bothering to look to see who had just spoken, "Look at their coats. Ponies are not supposed to have coats like that."

"They aren't? Everypony I've ever seen has coats like that."

"Oh, right," he said to himself, "This isn't my world. The rules are different here."

"Not your world?" the voice said, sounding slightly confused, "What do you mean by that?"

"Well, you see, I'm – Wait a minute," he suddenly interrupted himself, turning, "Who are you?"

Standing next to him was a bright pink pony with a large, wildly curly pink mane. "I'm Pinkie Pie," she said with a large smile, "Who are you?"

"Oh, yes right. How rude of me. I'm the Doctor," he said with a slight bow.

"The Doctor? That's kind of a weird name," Pinkie responded.

"Yes, well, I could say the same about yours," the Doctor replied, sounding slightly offended, "But that's beside the point. You're a pony, and you're talking. Do all ponies talk here?"

"Huh? Uh, yeah," the pink pony said, confused by the brown pony's question, "I mean, sure there are a few mute ponies, but for the most part, everypony can talk."

"I see. How curious," he muttered, looking at the ground thoughtfully.

"You okay mister?" Pinkie asked, sounding concerned, "You're acting kinda weird."

"Hmm, oh yes. I'm fine. Perfectly fine," the Doctor responded, with a small smile, "Anyway, could you tell me where we are?"

"We're in Ponyville!" the pink pony said, bouncing up and down slightly, "Well, we're not actually in Ponyville. We're on the outskirts of Ponyville, but we're close enough to Ponyville to technically be in Ponyville, even thought we aren't."

"Ah, yes, right. Um, no. I know that already," the Doctor said, glancing at the town, than back at Pinkie, "What I meant was, what planet are we on?"

"Planet? Uh, Earth," Pinkie said, even more confused.

"Earth?" the brown pony said, sounding just as confused as the pink mare, "Are you absolutely sure? Are you absolutely sure that this is Earth?"

Pinkie nodded slowly, saying, "Yeah. I'm pretty sure that this is Earth."

"That can't be," the Doctor said, looking back at the town, "There's no way this can be Earth. I mean, sure it looks like Earth, and it smells like Earth. It even tastes like Earth. But Earth is definitely not inhabited by multicolored, talking ponies."

"Uh, yeah, it is," Pinkie said, looking concerned, "I'm starting to think you're not okay."

"No, no, I'm fine, I'm fine," he replied, holding up a hoof, "The only thing wrong here is this world."

"What's wrong with the world?"

"Everything!" he exclaimed, looking at her, "The TARDIS coming here on seemingly on it's own, me being turned into a pony, ponies instead of people, HOOVES! It's all just wrong!"

Pinkie took a step back with a nervous chuckle, and said, "Yeah, you're definitely not okay. I'm gonna take you to the hospital."

The Doctor opened his mouth, but before he could say anything, there was a loud roar from nearby. The Doctor turned towards the sound, muttering, "Oh, that does not sound good. Apple Pie, I need you to listen to me very carefully," he said turning to Pinkie, "I'm going to go find out what's roaring out there. I want you to go back into town and tell all the ponies to get inside somewhere safe for a while. And do not follow me."

Then, without waiting for a response, he ran off in the direction of the roar, not looking back. Pinkie stood there, watching him go, a very confused look on her face, then after a moment, called out, "Wait! Who's Apple Pie?"

* * *

The Doctor ran as fast he could make his strange, new, four-legged body go, looking for the source of the roar. Luckily, there were more and more roars, allowing the Doctor to easily close in on the source. Finally, he found it and quickly dove into a large bush.

"Well, well, well," he muttered to himself, "Now this is interesting."

Close by to where he was, a large, creature stumbled about, seeming to be looking for something to eat. The creature stood at about seven feet tall and had grey leathery skin, with a row of spike running down the length of its spine. Its head looked vaguely pony like, with rows of long, sharp, jagged teeth, and it walked around on four, clawed hoof like feet.

"What is that?" a voice whispered from next to the Doctor.

"Well, that appears to be a Jallpurian hunter, but it looks very… pony like," the Doctor said, once again not looking to his side.

"A Jall-what now?"

"A Jallpurian hunter," he replied, "From the planet Jallpis. Very nasty, very dangerous, interplanetary predators. But this one looks like its been somewhat turned into a pony. Just what is wrong with this place…"

"Interplanetary?"

The Doctor nodded. "Jallpurian hunters can teleport themselves to other planets. Once there, they scour the planet, looking for anything that isn't big or strong enough to fight it off, and eat it. They do this for a while, than move off to another planet. Luckily, however, Jallpurians can't teleport to planets they've already been to. Eventually, they return home, where they proceed to reproduce and then die. As I said, very nasty, very dangerous, and ultimately, very odd."

"So, what do we do?"

"We need to find a way to get it off world. Once we do, it won't be able to come back and everyone here will be safe."

"I see. And how are we gonna do that?"

"Well, I do have a vague idea, but I'm not entirely sure how to pull it off."

"Ooooo… What's the plan?"

"Well, if I can get it to - Wait a minute," the Doctor interrupted himself again, turning, "Cherry Pie? What are you doing here?"

"Whose Cherry Pie? My names Pinkie Pie," the pink pony said.

"Whatever, that doesn't matter. Why are you here?"

"Well, I couldn't just let some crazy pony go running off on his own after some big scary monster."

"I told you not to follow me!"

"No, you told Apple Pie not to follow you, and I'm not Apple Pie. Who is Apple Pie anyway? Is she one of Applejacks cousins?"

"I – What? No, whatever. Just, go back home, get everyone to safety, and let me deal with this, okay?"

Pinkie shook her head. "No way. Like I said, I'm not letting some crazy pony I just met go off on his own."

"Gah! Fine! Whatever! Just, do what I say, and try not to get eaten."

"Okie Doki Loki! So, what's the plan?"

"We lure the Jallpurian to the TARDIS and I take it to some other planet."

"TARDIS? What's that? You mentioned it before, I think."

"It's a special machine that can travel to other planets, lets just leave it at that for now."

"Okie Doki Loki. But, how are we gonna lure it?"

"Like this," the Doctor said, and leapt out of the bush, shouting, "Hey! Jallpurian! Come and get me!"

The Jallpurian turned and roared at the Doctor, then charged at him.

"How is this a good plan?" Pinkie shouted as the two ponies ran away from the charging monster.

"When a Jallpurian sees prey, it chases it until it catches it!" the Doctor shouted back, "This way, we'll be able to get it to the TARDIS, and it wont go into town!"

"Okie Doki Loki, but where is this TARDIS thing?"

"Just follow me!"

The two ponies ran as fats as they could, the Jallpurian close behind, roaring as it ran. Finally, the Doctors large blue box came into view.

"There it is!" the Doctor cried out happily, "Oh, I am so happy to see you old girl! Just a snap of my fingers and…." The Doctor looked down at his hooves and growled. "Blast these hooves! Ok, Cherry Tart! New plan! Lead the Jallpurian off that way, while I get the TARDIS open!"

"Got it!" Pinkie called back and took off away from the TARDIS as the Doctor dove behind some trees. The Jallpurian, seeing only one pony, followed after Pinkie. Seeing the creature going away, the Doctor stepped back out and walked up to the TARDIS. Reaching into his saddlebag, he pulled out a small gold key and quickly unlocked the door.

"Okay! It's open now!" he shouted towards Pinkie, "Lead it back this way!"

Pinkie and the Jallpurian came running back, headed straight for the now open door. Pinkie rushed inside, and the Doctor quickly dove in after her, shutting the door. The Jallpurian kept running and slammed into the TARDIS, causing the whole thing to shake.

Inside, the two ponies lay on the floor, out of breath and breathing heavily.

"Well… That was close," the Doctor panted, standing up, "We're safe now. Anyway, Coffee Cake, welcome… To the TARDIS."

Standing up, Pinkie looked around the impossibly large room, eyes wide. "Whoa…" she said, "The inside is… and the outside is… Oh! I get it!"

"I – What?" the Doctor asked, confused.

"The inside isn't really the inside. Because there isn't an inside. The outside is just a door and this is somewhere else."

"Yes… That's right. How did you…?"

"It's super easy to see when you don't think about it," she replied matter-of-factly.

"My God…" the Doctor mumbled after a moment, "Did anyone ever tell you that you are brilliant?"

Pinkie shook her head. "Most ponies just think I'm crazy."

"That's not such a bad thing. Most geniuses are a little bit crazy. Just look at me."

Pinkie giggled and said, "So what do we about the jelly bean thing Mr. Genius?"

"Well, we need to get in here, but as it is right now, it'll eat us on sight, so we need some way to make sure that doesn't happen."

"We could wait until it falls asleep."

The Doctor shook his head. "Jallpurians don't sleep. It's one of the things that makes them so dangerous."

"Is there some way we could, like knock it out?"

"Knock it out? Oh Bubble Berry! You are a genius!" the Doctor exclaimed, "Yes! Oh, silly Doctor! Why didn't I think of that before?"

"It's Pinkie Pie," the pink pony responded, "And why am I a genius this time?"

"Because there is a way to knock out the Jallpurian. With strawberries."

"Strawberries?"

"Strawberries," the Doctor nodded, looking a little smug, "They grow all over the universe. A rather universal fruit, if you will. And of all the things in the universe that they can eat, Jallpurians love strawberries most of all. However, they almost never eat them."

"Why not?"

"Because if they do, it causes them to fall unconscious for about twelve hours. No idea why. It just happens. I think it's some kind of allergy."

"So if we can make the jalopy eat some strawberries, then we can get it in here safely."

"Exactly! And I do believe that I have some strawberries in the kitchen. If you'll wait here for just a moment, I'll be right back."

The Doctor rushed off into another part of the TARDIS, leaving the pink pony sitting alone. Then, from where he ran off to came a clattering sound and the Doctors voice, saying, "No. No, not that either. Ew, no! Gah, how long has that been in there? Definitely not that. Ah ha! There you are!"

The Doctor came walking back out with a small plastic bag of strawberries in his mouth and set it down in front of Pinkie, smiling.

"Hurray! Strawberries!" Pinkie exclaimed jumping into the air.

"Indeed. Now we just need to get these to the Jallpurian."

"How are we gonna do that?"

"Simple Cheese Cake. We throw it outside."

"But if we do that, won't the jabally thing get in here? And my names Pinkie Pie."

"Not if we time things just right. Come on," the Doctor said, ignoring Pinkies last statement and walking over to the console. He set to work pressing buttons and pulling levers, and a screen dropped down, showing the Jallpurian outside, pacing around, and then ramming into the TARDIS, causing the room to shake. "With this," the Doctor smiled, "We can watch it and time things out just right. Now then, you stand here and watch the screen. I'm gonna go stand by the door, and when you see the Jallpurian move back, tell me so that I can throw the strawberries outside."

"Okie Doki Loki!" Pinkie replied with a salute and stood in front of the screen as the Doctor took his place by the door. Pinkie watched the screen, starring intently at the creature mulling about outside. Then, as it began to move backwards, Pinkie called out, "Now!"

"Right! Take this Jallpurian!" the Doctor shouted opening the door and throwing the bag of strawberries outside.

On the screen, the two of them could see the Jallpurian stop and look down at the bag, confused. It bent its head down and sniffed at the bag, then snapped it up, quickly swallowing it whole. It prepared to ram into the TARDIS again, then stopped, stumbling groggily and than fell over.

"Yes! We did it!" the Doctor exclaimed, punching a hoof in the air, "Ha ha! Even with hooves, I've still got it!"

"Hurray!" Pinkie exclaimed as well, doing a back flip.

"Now then, lets get that alien predator on board."

* * *

It was a little difficult, with how much the Jallpurian weighed, but the two ponies were able to get it into the TARDIS. With the unconscious creature now safely inside the Doctors strange blue box, the two stood outside.

"Well, this has certainly been an interesting day," the brown pony said.

"I know!" Pinkie bounced up and down, "I've never had so much fun in all of my life! You may be a little crazy, but you sure know how to have a good time!"

"Thank you. Now then, there's one last thing I need you to do."

"Sure thing! What is it?"

"I'm gonna take the Jallpurian to a different planet, and I want you to stay here, alright? I'll be back in moment, so just stay here. Okay?"

"Got it," Pinkie responded with a nod.

"Good," the Doctor smiled and walked back into the TARDIS. With in a few seconds, the blue box started to make a soft whooshing sound and began fading into invisibleness. Within a matter of seconds, it was gone. Pinkie simply stood there, staring with wide eyes, mouth hanging open, struck speechless for the first time in her life. Then, only a few seconds later, the whooshing returned and the TARDIS reappeared. The door opened and the Doctor stepped back out. "There. All done," he said.

Pinkie stared at him, still speechless. It took her a moment, but eventually, she found her voice again. "Wow," was all she could say.

"Indeed. Now then, while I was away, I took a little bit of time to see why I ended up here. Seems a freak wormhole opened up around the TARDIS while I was trying to reach London and funneled me here. I was able to lock onto what I think is that same wormhole, and I'm pretty sure I can use it to get back to my world. So, with that said, I just want to say, thank you for all your help today Pinkie Pie."

"You… You got my name right."

"Oh, have I been saying it wrong? Dreadfully sorry. Anyway, once again, thank you. This is good-bye. May we somehow meet again in the future."

"Good-bye Doctor," Pinkie replied with a sad smile as the brown pony stepped back into the TARDIS. With a whoosh, the TARDIS faded away and Pinkie was left alone in the clearing. "I'm gonna miss him," she said and began walking back towards town. She suddenly stopped, hearing a familiar whoosh coming from behind her. Turning, she saw the TARDIS reappear.

The door opened and the Doctor stepped out and with a smile said, "Hello, London! It's good to be… Right where I was. What? How is this even…?"

"Doctor!" Pinkie exclaimed, rushing forward and pulled the brown pony into a tight embrace.

"Pinkie? What are you doing here? Have you just been hanging around here this whole time?"

"Huh? What do you mean? You've only been gone for a few seconds."

"Wait, really?" the Doctor asked, pulling himself out of Pinkie's hug.

Pinkie nodded. "What happened you to going back to your own world?

"I don't know," the brown pony said confusedly, "I thought for sure I was headed home, but apparently, whatever I locked onto wasn't a wormhole. I'm starting to think it was just an empty part of space…" the Doctor trailed off, look away, lost in thought.

"So, what now?" Pinkie said after a moment, pulling the Doctor away from his thoughts.

"Hmm? Oh, well, I guess I go exploring. This is a whole new universe for me, completely different from my own. I would rather like to see it. And, I could use a companion."

"You want me to come with you to see the universe?" Pinkie said incredulously.

The Doctor nodded. "Not just the universe. The TARDIS, my wonderful, beautiful machine, can travel, not just through space, but also through time. So you see Pinkie, if you come with me, we won't just be traveling to planets and places you've never heard of, we'll also be traveling into your past and future! So, what do you Pinkie Pie? Want to come along? Pinkie Pie?"

The Doctor looked around the clearing, and could see no sign of the pink mare. "Pinkie?" he called out, "Pinkie, where are you?"

"Come on Doctor! We're wasting time!" Pinkie's voice called out from within the TARDIS.

The Doctor turned to look at the blue box and chuckled. "Well, I guess that's a yes."

* * *

Thanks for reading, and be sure to leave a nice review!


	2. Go Ask Alice

I don't own My Little Pony or Doctor Who or any of their related characters in any way, shape, or form.

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Chapter 2 Go Ask Alice

"Alright Pinkie Pie," the Doctor said, walking into the TARDIS, "Thousands of planets, countless points throughout time and space. Where should we go first?"

"I've always wondered what Ponyville would look like in the future!" Pinkie cheerily replied, bouncing up and down, "Lets go there first! Lets go there first!"

"Ponyville in the future, eh? Sounds good. How far in the future do want to go? Oh, how about three hundred years? I've always liked the number three hundred."

"Lets do it!"

Moving up to the center console, the Doctor began to press buttons and pull levers, saying, "This should be good. I didn't get a chance to see Ponyville, what with the Jallpurian, so this'll be an excellent opportunity for me." As he spoke, the TARDIS made whooshing and grinding noises, then abruptly stopped. "And here we are," the Doctor said.

"Wait, what?" Pinkie asked, looking at the Doctor, "But we didn't move."

"Faith, my dear Pinkie Pie. Take a step outside, and meet the future!"

"If you say so."

Pinkie opened the front door and stepped outside, looking around. "It looks the same Doctor!" she called back.

"Maybe so, but this is the future," the Doctor replied, stepping outside as well.

"Take me somewhere else," Pinkie said, turning to the brown pony.

"What? We just got here!"

"And now I want to go somewhere else."

"Oh come on! Lets just walk around town a little. I didn't get to see it before. You live here. You could show me around a bit, then we can go somewhere else."

"Ok, fine," Pinkie said, "You're lucky I like giving tours of Ponyville."

The two ponies walked around the town for while, Pinkie pointing out the few buildings she recognized from her time. The town, while looking mostly the same, had changed. Several shops and houses had been remodeled, the buildings now housing new businesses and services. Very few looked the same, with small plaques stating that they were historical sights where important ponies had lived, or an important event had happened.

"And that's pretty much all there is," Pinkie said as they finished up.

"Wow," the Doctor replied, "This is an absolutely beautiful town!"

"Yep! Now lets go."

"Go? Oh, yes right. Somewhere else. Let's be going then."

The Doctor started walking back towards the TARDIS, Pinkie following close behind, then stopped, seeing something interesting.

"Pinkie, look over there," he said pointing.

Pinkie looked at where the Doctors hoof was pointing and saw a blue colt, sitting on a bench. He was bit far away, but from what they could see, he appeared to be softly crying.

"Lets go see what's wrong with him," the brown pony suggested, "We might be able to help."

"Ok, but only because I can't stand to see anypony sad," Pinkie agreed.

Making their way over, they could see that the colt was young, a foal, with a short grey mane and tail.

"Hello there little guy!" the Doctor said as they got closer, sitting down next to him, "Is something wrong?

The colt looked up at him sniffling. "Who are you?" he asked.

"Oh, how rude of me. I'm the Doctor. What's your name?"

"Toby," the colt replied.

"Toby? That's a good name."

"Good? It's weird!" Pinkie said.

Toby looked over at Pinkie, saying, "And who are you?"

"My names Pinkie Pie," she replied with a smile.

"That's an old mare's name!" Toby said, laughing.

"What!" Pinkie yelled, offended.

"Sorry," Toby replied, "It's just, only old ponies have names like that."

"Well, I never," Pinkie turned away and stuck her nose into the air, "Lets go Doctor."

"Hold on a moment Pinkie. Something is troubling young Toby here, and we have an obligation to help him out."

"You do?" the young pony asked, looking slightly confused.

"Of course! I'm the Doctor. It's what I do," the Doctor smiled, "Now then, what seems to be the matter?"

"It's my sister, Alice. She disappeared a few days ago and nopony can find her anywhere."

Pinkie gasped loudly and turned back around. "Oh no! That's terrible! What happened?"

"I don't know…." Toby said, eyes beginning to tear up.

"It's okay Toby," the Doctor said, placing a hoof on Toby's shoulder, "Tell me about the day she vanished. Did anything strange happen?"

Toby shook his head and rubbed his eyes. "No, it was normal day."

"When exactly did she go missing?"

"The middle of the night, I think."

"What makes you say that?"

"Because when I woke up, her bed was empty. We sleep in the same room, so I always see her when I wake up."

"Curious," the Doctor muttered to himself, "Plucked out of bed in the middle of the night. I wonder…"

The Doctor looked away for a moment, deep in thought, then turned back to the young colt. "I'd like to take a look around your room, if that's okay with you."

"Sure," Toby replied with a nod, "If it'll help you find my sister, I'll do anything."

"Splendid!" the Doctor said, standing back up, "Lead the way my good sir!"

* * *

The trip through town was short, as Toby's house was only a dew blocks away from the park. His house was a small single story building. "It's not much, I know," he said, "But it's all mommy and daddy can afford."

"It's not so bad," the Doctor said, "I rather like it. It has a nice quaint charm."

Pinkie nodded her head in agreement. "Just cause it's small doesn't mean it's bad. You should see the Doctors house! It's way smaller then this, but it's the coolest house ever!"

"Really?" Toby said, eyes wide in amazement.

"Well, I don't know if it's the coolest ever, but it certainly is cool."

"Wow. I'd love to see it!"

"Don't you worry, I'm sure you'll get to see it soon enough. Now then, if you could direct us to your bedroom, I can get started."

Toby nodded and led them inside. The house was empty of other ponies. Toby explained that both his parents were at work right now. They made their way down the hall and entered into a small room. Two beds sat inside, pressed up against opposite walls, with a small nightstand next to each. One had a small desk lamp and some books on it, and the other was covered in various toys.

"I take it that ones Alice's," the Doctor said, pointing to the one with the books.

Toby nodded. "Alice is really smart and loves reading all kinds of books."

"She sounds a lot like Twilight," Pinkie said.

"Who?" the Doctor said, looking at the pink mare.

"Just one of my friends. It's not important right now. We need to find Alice."

"Right. Glad to see you're finally on board Pinkie Pie."

"Like I said before, I can't stand to see anypony sad."

The Doctor nodded his head and walked over to Alice's bed. Reaching into his saddlebag, he pulled out a small metallic tube with a small light bulb on one end.

"What's that?" Toby asked.

"This is my sonic screwdriver," the brown pony replied with a smile.

"What's a sonic screwdriver?" Pinkie asked.

"Well, it's lot like a normal screwdriver, just a bit more… sonic," the Doctor tried to explain, but seeing that his two companions looked even more confused, sighed. "Here, just watch."

Pointing the sonic screwdriver at the bed, the Doctor pressed small button, the bulb lighting up and it began to make a buzzing sound. The Doctor waved it about, and looked back at the two ponies. "The sonic can do all sorts of things, like locking and unlocking doors, as well as analyzing energy readings and signals."

"Is that what you're doing right now?" Toby asked, "Looking for signals or whatever?"

The Doctor nodded and turned the sonic off. He held it close to his face and looked at it intently for a few seconds before saying, "And it appears I found one. There are faint remnants of teleportation energy all around the bed. It seems that your sister was teleported away from here."

"Teleported? By a unicorn?" Toby asked.

The Doctor turned to Toby, eyes wide. "Did you just say unicorn?"

Toby nodded. "Yeah, why?"

"Are you telling me that there unicorns in this world?"

"Uh, are you okay?" Toby asked, sounding very concerned.

"Don't worry, he's fine," Pinkie said, "And yes Doctor. There are unicorns here. Pegasai too!"

"My word. I… I don't know what to say. This is amazing. Pegasai and unicorns! Simply amazing!"

"Doctor, the signal?" Pinkie said.

"Hmm? Oh yes, right. Um, no it wasn't a unicorn," the Doctor chuckled, "Unicorns. Amazing. Anyway, whatever took Alice appears to be alien in origin."

"Aliens took my sister?" Toby asked, skeptical.

The Doctor nodded. "Yes. And I think I might know who."

"How?" Pinkie asked.

"There are many, many different kinds of teleportation technology, used by different races. Each one uses different kinds of power sources and slightly different means of achieving the teleportation. Because of this, whenever they send someone somewhere, or pull something to them, it leaves behind trace energy that is very unique. By analyzing the energy, one can figure out exactly who did the teleporting."

"So who is it?" Pinkie asked.

"Well, I can't be certain until I run a proper scan back at the TARDIS, as the energy is very faint and I can only seem to get a reading on a very small portion of the overall energy signature," the Doctor said, putting the sonic away, "What I can see is a fairly common kind of background radiation that shows up in a few different teleportation signals."

"Well then, we should back to the TARDIS, right?" Pinkie asked.

The Doctor nodded. "Exactly right. Come along you two," the Doctor said as he left the room, "We have a pony to find."

* * *

"Here we are," the Doctor said as they came up to the TARDIS.

"And where are we exactly?" Toby asked.

"This is the TARDIS. Remember the house Pinkie mentioned? This is it."

"Well, it certainly is smaller then mine. It doesn't look like you can even fit in there."

"Oh, you would be surprised at what can fit inside. Go on in."

"Um, okay," Toby said pushing open the door and stepping inside.

The Doctor and Pinkie followed him in. Toby stood just inside the door, eyes wide, mouth hanging open.

"So, what do you think?" the Doctor asked.

"It's… It's so much bigger on the inside," the young pony stammered.

"Oh, I never get tired of hearing that," the Doctor said smiling, "Welcome to the Time and Relative Dimension in Space, or TARDIS for short."

"Is that what it stands for?" Pinkie asked.

"Yes. Didn't I tell you?"

"Nope," Pinkie replied, shaking her head.

"Oh, well… There you go," the Doctor said, making his way to the console and placing his sonic into a small slot, "Alright, lets see what we got." The Doctor began typing away at the keyboard. "Hmm, well now that's interesting," he finally said after a moment.

"What is it?" Pinkie asked, moving to stand beside him.

"The TARDIS was able to detect a few more bits of the energy signature, but it could get the whole thing."

"What's that mean?" Toby asked.

"Well, it narrowed down the list of potential races who could've taken your sister, and, while that's admittedly good, it puts us right back where we were before."

"Oh," Toby said, looking at the ground.

"Don't you worry Toby," the Doctor said, "While running the scan, the TARDIS detected the same signal from somewhere close by. A town called," the Doctor looked at the screen and sighed, "Fillydelphia. Really? Oh, this world."

"Does that mean that whatever took my sister took somepony from there?" Toby asked.

"That is the most likely conclusion. Not only that, but the signal should be much fresher. I'll be able to get a much better reading off of it, and should be able to pinpoint just who it was. And who knows, maybe I can get a lock on their ship as well."

"Then that means we can save her, right?" Toby said excitedly.

"Yep," the Doctor nodded, pressing buttons and pulling levers. There was a whoosh, some grinding, and when it stopped, the Doctor turned to the two ponies behind him. "Lets go see what we can find."

The three of them walked out of the door. As soon as they stepped outside, Toby stopped and gasped. "We… We're in Fillydelphia…. But, how did we…?"

"I know. It's awesome, isn't it?" Pinkie said smiling.

"Yes, amazing, I know," the Doctor said moving past them, "And while I would love to stand around admiring the TARDIS, we have a much bigger issue at hand right now."

"At hoof," Pinkie interrupted.

"Sorry?" the Doctor said, turning to look at her.

"We have a much bigger issue at hoof," she replied.

"Is that really what you say here?"

The two ponies nodded, and the Doctor began to laugh. "Issue at hoof. Oh, this world…. Yes well, as I was saying, we have a much bigger issue at hoof right now. We need to find that signal. And we need to find it fast."

"Right," Pinkie nodded, "Lets get going then."

"Yeah!" Toby said excitedly, "Lets get my sister!"

"That's the spirit! Come on then! Vamos!" the Doctor said as he began to move again, than stopped, "Vamos? Ugh, no, that's terrible. No, no, bigger issue at hoof. Lets just be on our way."

"You sure he's okay?" Toby whispered to Pinkie as they followed the Doctor.

"I'm starting to think no," the pink mare replied.

* * *

The trek through the city was a strange one. Pinkie and Toby followed the Doctor as walked down streets seemingly at random, pointing his sonic screwdriver everywhere, and even doubling back upon his path several times. Finally, after what felt like hours, the came to a stop in front of large two-story house.

"Here we are," the Doctor said, looking up at the house, "This is where the signal is. Lets go in."

"Wait! This is someponies house Doctor," Pinkie said, "We can't just barge in there."

"Yes I know that," he replied, "I do think about these things you know."

"Then you have a plan?" Toby asked.

The Doctor nodded and walked up to the house. "Just follow my lead," he said and knocked on the door.

The door opened a moment later and they were greeted by a brick red unicorn. "Yes, can I help you?" he asked.

The Doctor pulled a small brown wallet from his saddlebag and held it open. "I'm detective John Smith. These are my assistants Pinkie Pie and Toby," he said gesturing to the two ponies behind him, "We're investigating the disappearances around Equestria."

"You're with the police? Then you're here about Emily, right?" the unicorn said, sounding excited.

"Yes. We're here about Emily. May we come in?"

"Yes, of course! Please, come in. Come in," the unicorn said, ushering the three of them inside.

"Doctor, how do you have a Fillydelphia police badge?" Pinkie whispered as the entered.

"I don't," he replied, opening the wallet, revealing a small piece of blank white paper, "This is psychic paper. Shows people whatever they want to see."

Pinkie looked at the paper, then shrugged. "It just looks blank to me."

"Hmm, how curious," he muttered, putting the wallet away.

The red unicorn led them down a short hallway and into a sitting room. A white unicorn sat on a couch, her back to them. "Honey, there's some ponies with the police here," he said, moving over to her.

The white unicorn turned and they could see that her eyes were red and puffy from crying and her cheeks were tear streaked. "Are they here about Emily?" she asked.

"Exactly right madam," the Doctor said, "Would you permit us to ask you a few questions?"

She nodded. "Yes, of course. Anything to get my little filly back."

"Right. Ok, lets see. When was it that your daughter disappeared?"

"Two days ago."

"Did anything odd happen on that day?"

"No," her husband responded shaking his head.

"And when exactly did she go missing?"

"During the night."

"What makes you say that?"

"Emily didn't come down for breakfast, so I went to see if she was okay and her room was empty."

"I see. Excuse us a moment," the Doctor said, turning to his companions. "What do you think?" he asked in a hushed voice.

"Sounds just like what happened to Alice," Toby said.

"Down the last detail. Normal day, then she goes poof in the middle of the night."

"So it's the same guys then?" Pinkie asked.

"That's looking more and more like the case every second." The Doctor turned back to the unicorns, saying, "I'd like to take a look at Emily's room, if that's alright."

"Of course," the white unicorn said.

"Thank you miss…"

"Susan," she replied.

"Thank you Miss Susan. Pinkie, you stay here and ask some more questions."

"Wait, why me?"

"Because I need to look at the room and Toby's a bit to performing an interrogation."

"Alright fine."

"Thank you. If you could lead way my good sir?" he said to the red unicorn.

"Yes, of course. This way," he replied leading them to a door upstairs. "This is Emily's room," he said as they approached it.

"Thank you for leading the way mister…"

"David."

"Yes, thank you David. We can take it from here."

"Sure," David said, heading back downstairs.

"Alright Toby, lets get to work."

* * *

The three ponies made their way away from the house about twenty minutes later.

"Well, that went okay, I guess," Pinkie said.

"Okay? It went better then okay! Those were unicorns!" the Doctor exclaimed happily, "Actual unicorns! You were right Pinkie Pie. Now if I could just see a pegasus…."

"Uh, Doctor, what about my sister?" Toby asked.

"Hmm? Oh yes, right. There was, as I suspected, much fresher teleportation energy in Emily's room, and I was able to get a full signal. Once we get back to the TARDIS, I'll be able to find out just who is behind all of this."

"And then we can save Alice?"

"Yes Toby. Then we can save Alice."

"Thank you so much Doctor!" the young pony exclaimed.

"Don't thank me quite yet Toby," the Doctor replied, "We still have to analyze the signal."

They continued forward for a few minutes in silence before the Doctor noticed something odd.

"Pinkie Pie, are you okay? You've been awfully quiet for while. Pinkie Pie?" He looked to his right and saw that the pink mare wasn't there. "Pinkie Pie!" he called out looking around, "Pinkie Pie, where are you!"

"Doctor, where did Pinkie go?" Toby asked looking around as well.

"I don't know Toby. I don't know."

* * *

Thanks for reading and be sure to leave a nice review!


	3. The Belly Of The Beast

I don't own My Little Pony or Doctor Who in any way, shape, or form.

* * *

Chapter 3 The Belly Of The Beast

"No, no, no!" the Doctor panicked, looking around, "This is not good. This is not good!"

"Doctor where is she?" Toby said, starting to panic as well.

"I don't know Toby! I don't know! Oh, I hate it when I don't know!" The Doctor continued to look around, with frantic breaths, before shouting, "PINKIE PIE!"

Somehow, seemingly against all logic, the hyperactive pink mare was gone. Vanished into thin air, without leaving any sort of clue behind.

"No. Please no," the Doctor said quietly to himself, "I can't have lost her. Not this early. She has to be here somewhere."

"Doctor, I don't like this," Toby said.

"I know Toby. Believe me I know. We have to find to Pinkie."

"What about my sister?"

"Yes, finding Alice is still a top priority. But first we need to… Wait a minute," the Doctors eyes went wide and large smile appeared on his lips, "That's it. That's it! Oh Toby, you are a genius!"

The Doctor pulled out his sonic screwdriver and ran back the way they had just come from, waving it in every direction, muttering, "Come on, where are you…"

"What's going on? What did I say?" Toby called out confusedly as he gave chase.

The Doctor finally stopped, and turned to the young colt, smiling broadly. "I know where Pinkie Pie is!" he exclaimed proudly.

"You do? Where is she?"

"With your sister."

"My sister? Then that means… The aliens took her?"

The brown pony nodded. "Exactly. When you mentioned Alice, I remembered that she was teleported away, so I retraced our path, looking for traces teleportation energy. And I found some right here. But it's not just any old teleportation energy. It's an exact match for the energy I found in Emily's room."

"That can't be right," Toby said, frowning, "The guys that took Alice took her at night. And the same thing happened to Emily. But Pinkie just got taken in the middle of the day."

"Quit true Toby, quite true. But it most definitely was the same aliens. The energy signal doesn't lie."

"Well, why did they take her then?"

"That's easy," the Doctor replied with a smile, "They wanted to send me a message."

"A message?" Toby asked confused.

"The fact they took Pinkie shows that they're watching the planet right now, keeping an eye on things. They saw that I was poking around, looking into what happened. They must have realized that I could not only figure out what happened, but also stop them. So they had to try to stop me."

"I'm still not sure I understand."

"Alright, think about this way. Let's say you're the aliens. You're taking ponies for whatever reason, and you see someone who can stop you. What would you do?"

"Stop them, I guess."

"Right. And how would you do that?"

"Take them?"

"Exactly."

"But, they took Pinkie, not you," Toby said, still sounding confused.

"Which brings us back to the message," the Doctor smiled, "By taking Pinkie in broad daylight, they're telling me that they can take anyone they want, at anytime they want, from anywhere, and that if I don't back off, they'll take me too."

"Oh. I see," the young colt said, finally understanding, "So, what do we do now? We can't back off. We need to save Pinkie and my sister and everypony else that they took."

"Not to worry my young friend. No alien's gonna scare me off that easily," the Doctor said, a fierce smile crossing his face, "We need to get to back to the TARDIS quickly so that I can find them. And when I do… Come on Toby. We're wasting time."

"Uh, right," Toby said. The Doctors sudden and unexpected intensity scared the young colt, but it quickly passed. He followed the brown pony as they began to head back to the TARDIS, slightly keeping his distance.

* * *

When they finally reached the blue box, the Doctor went straight to the center console and placed the sonic into the same slot he had before. He began typing away on the keyboard, muttering to himself. After a minute or so, the Doctor turned, smiling. "Got it," he said.

"You found them?" Toby asked excitedly.

"Kind of. I've finally been able to determine just who it was that kidnapped your sister and Pinkie Pie."

"Who is it?"

"The Klandians. I can't believe I didn't see it before though. It's all so obvious now…"

"Why's that?"

"The Klandians are one of the strangest races of aliens in the entire universe. For whatever reason, the entire species is male. Absolutely zero female Klandians exist. So they travel the universe kidnapping young girls so that they can reproduce."

Toby just stared at the Doctor, mouth-hanging open, horrified by his words.

"Not like that," the brown pony said, holding up a hoof, "They reproduce using estrogen."

"What's estrogen?" the young pony asked confused.

"A hormone produced by female brains. You see, they kidnap young girls, hook them up to a nasty machine, and drain the estrogen from them for few years until they die."

"There's still time to save them then!"

The Doctor nodded. "There's just one problem. I can't find the ship."

"What do you mean?"

"Well, I thought by finding a fresh teleportation signal, I could trace it back to the ship, but it would appear that they have protected themselves from that sort of detection. The only way we'll be able to find them now is if we were receive a direct transmission from them, but the chances of that happening are astronomical at best."

Toby's face fell and he looked at the ground. "So what do we do now?"

The Doctor sighed and shook his head. "I'm not sure Toby. The Klandians don't want to be found, that much is obvious. And if we can't figure out how to find them…."

"We can't give up hope! There has to be something we can do!"

"But what? I can't track the teleportation energy and the chance of receiving a transmission from them is so small, it's almost nonexistent. There's nothing we can… Wait. Tracking teleportation. That's it! That's how we can find them!"

"Huh? But you just said that we can't track the teleportation energy."

"You're right, we can't track the energy, but we can track what's teleported."

"How?"

"All we have to do is put a tracking device onto whatever the Klandians take next and we can follow the signal right into the heart of their ship."

"How do we do that? We don't know who their gonna take next."

The Doctor sighed and turned away. "Actually, we do."

"Who is it?"

"I'm very sorry. I wish there was some other way to do this. I really truly do."

"Who is it Doctor?" Toby said very forcefully.

"It's you Toby. The Klandians are going to take you."

* * *

Pinkie blinked several times as she looked at her new surroundings.

"What the…?" she said confusedly, "Doctor, what just happened? Doctor?"

She looked over to her side and saw that neither the Doctor nor Toby were there.

"Doctor? Toby? Hello? Is anypony there?"

She continued to look around, desperately trying to find them. Wherever it was that she was now, it was definitely not Fillydelphia. In fact, it wasn't anywhere that Pinkie recognized. It was a large room. The walls, ceiling, and floor appeared to be made of metal. Large tubes ran down the one of the walls, connecting to a large round platform on the floor that she was standing on. On the wall opposite her was a large rectangular door.

"Where am I?" she wondered aloud.

The door opened and a short creature walked in to the room. It walked on two legs that ended in hooves, as did its arms. It's head looked like a pony's, but looked… off. It was too round and the muzzle was too short. It wore a shiny black suit with small blinking lights all over it. The creature looked at Pinkie and opened its mouth, making a series of popping and clicking sounds.

"What?" Pinkie said after a moment.

The creature cocked its head to the side and narrowed its eyes at her. It made the same series of noises, somehow sounding slightly angry this time.

"I have no idea what you're saying," Pinkie replied.

The creature growled softly and left the room. A moment later, a different creature entered the room, this one slightly taller then the other one.

"I apologize for Bramkin," it said haltingly with an odd accent, "We sometimes forget that our captives do not speak our language. I am Grikin."

"What's going on here? Where am I?" Pinkie demanded.

"This is our ship. You are our prisoner," Grikin said stepping forward, "You are to going to be harvested."

"Harvested? That doesn't sound good."

"Oh no. It is very good. For us," Grikin replied with a wicked smile, "You see, we need your estrogen in order to survive as a race."

"My what now?" Pinkie asked confused.

"Estrogen. It is a, um… what is the word in your language? Chemical? Yes, chemical, produced in the brains of your kind."

"Ponies?"

"Females."

"That's why you took Toby's sister and that other filly, isn't it?"

"Along with several other of your kind."

"Yeah, well, I won't let you take it! I'm using my estro-whatever… I think, so you can't have it!" Pinkie said rather forcefully.

Grikin produced a wet gurgling sound that seemed to be laughter as the door behind him opened and two more creatures entered the room. "You do not have a choice."

* * *

"What do mean they're gonna take me next?" Toby demanded, "You can't be serious! I'm not gonna let those monsters take me!"

"Do you really think I would be suggesting this if there was another option?" the Doctor replied, not looking Toby in the eye, "I don't like this any more than you do."

"That's easy for you to say!" Toby interrupted, "You're not the one who's getting kidnapped!"

"Toby, please, just calm down," the Doctor said, turning towards the young colt.

"No! Just shut up!" Toby yelled, "Just… just shut up and leave me alone!"

"Toby, no… I…."

"Just stop it you jerk! I never should've trusted you! You said you could find my sister and instead we've just been floundering around in circles! Just take me back to Ponyville and go away! I'll find Alice on my own!"

The Doctor sighed and turned around. "If that's what you really want. Just, let me say one thing before we go."

"Fine," Toby said, glaring at the brown pony.

"If you really are serious about looking for Alice on your own, the Klandians will still take you."

"What? No… You're lying. You're just trying to stop me from going."

"Really?" the Doctor said turning, face cold and intense, "You really think I do that? You really think I would be that petty?"

Toby looked away, not wanting to meet the Doctors gaze.

"Do you remember why the Klandians took Pinkie? It was to get us to stop poking around. What do you think will happen to you when you go off on your own? That the Klandians will leave you alone? They will take you Toby. There is no way around that. No matter how much we may wish it, there is no way around it. So we might as well make the most of it."

Toby nodded his head, still not looking at the Doctor. "You're right," he said quietly, "I'm sorry. I didn't mean what I said. I was scared and angry."

The Doctor's expression softened and he placed a hoof on Toby's shoulder. "It's alright," he said, "I know you didn't mean it."

"So what do we do?" the young colt asked looking at the Doctor.

Turning back to the console, the Doctor pressed a few buttons and a small silver disc about the size of a dime was produced. Picking it up he turned back to Toby. "I place this tracker on you and when you're taken, I follow its signal to the Klandian ship and save everyone that's been taken."

"You're sure that'll work?"

"Trust me," he replied with a smile, "I'm the Doctor."

* * *

Pinkie was ushered through the ship rather forcefully. She passed by several other Klandians, all at various consoles and controls, running the many different aspects of the ship. Finally, she was brought into a very large room. Several other female ponies were in the room. All of them were floating in large glass tubes filled with a clear liquid. Some kind of metal helmet was on their heads with several smaller tubes coming out them and running to the top of the larger tube.

"What is this place?" Pinkie asked, eyes wide, as she looked around.

"This is the harvesting room," Grikin said, "This is where we will take your estrogen." Grikin then made a series of pops and clicks and pointed to an empty tube.

The other Klandians nodded and moved Pinkie towards it. "No! Stop!" Pinkie cried, trying to get away.

Grikin laughed again. "Do not struggle. Everything will be fine. The harvesting process is painless. It will be like you are sleeping."

"I don't care!" Pinkie yelled, still struggling, "I won't let you take my estro-stuff!"

Grikin sighed and moved over to Pinkie. "I already told you. You do not have a choice," he said, pressing a few buttons on the keypad in front of the tube. An opening appeared in the glass and Grikin looked directly into Pinkies eyes. "Good bye my dear. Your estrogen will make many new Klandians."

Just before Grikin could push Pinkie into the tube, the door suddenly opened and a Klandian rushed in, popping and clicking franticly. Grikin responded and the Klandian spoke franticly once again. Grikin growled and pressed a button, closing the tube. "It would seem that you will get to live a short while longer," he said, somewhat angrily, "I must go deal with that little blue pony that was with you."

"You mean Toby?" Pinkie asked, looking at Grikin.

"I do not care what his name is. He did not heed our warning like the other one did, so now we must bring him here."

"What are you going to do to him?" Pinkie asked worried.

Grikin smiled wickedly as he turned to leave the room. "You are better off not knowing."

* * *

"Are you ready?" the Doctor asked.

Toby looked at the TARDIS doors and shook his head. "No. But I have to do this."

"Alright. Let's do it then."

Toby nodded and headed outside. Hitting a few buttons and pulling few levers, the Doctor brought down a screen. On it, he could see Toby walking away from the TARDIS. Pressing a few more buttons, the screen showed him the location of the tracker hidden within Toby's mane.

"Alright Toby," the Doctor muttered to himself, "I sure hope this works."

The Doctor watched the screen for several minutes, as Toby made his way through Fillydelphia. Then, very suddenly and without warning, Toby vanished.

"Took the bait I see," the Doctor said. Typing away furiously at the keyboard, the screen changed once again, showing a small red blip out in the middle of space. "Found you," he said with a fierce smile, "Alright. Time to make a house call. Huh… Time to make a house call… Still not quite it…."

The pulled a few levers and pushed a few buttons. The TARDIS whooshed for a few seconds and when it stopped, the Doctor turned to the door. "Lets go."

Pushing open the doors, the Doctor found himself in the middle of the Klandians control room, with several very surprised Klandians staring at him and the TARDIS.

"Hello there!" he called out cheerily to them, "I'm the Doctor. Nice to meet you all. You're probably wondering how I got in here. Well, lets just say I had a little help from my friend Toby."

"The blue one?" one of the Klandians asked.

"The very same. Now then, you lot took my friend Pinkie Pie, as well as several other ponies, and I will not stand for that. Release all the ponies you've kidnapped from your machines and let them go free. Then, once you've done that, leave this ship and go back to your home planet. Because once I've returned your captives to their homes, I'm going to come back here and get rid of your ship forever. And if I see any of you on board, even if it's just one, then I will make your entire race, past, present, and future, wish that you had never, ever even heard of this planet. Because I am the Doctor! And I do not take kindly to people who hurt my friends."

The Klandians looked around at each other, then to the one who had spoken. He stepped forward and laughed. "We are not scared of your threats Doctor."

"No? Well, you should be."

Acting quickly, the Doctor pulled the sonic screwdriver from his saddlebag, pointed it at the ceiling and turned it on. When he did, all the Klandians shrieked in pain and fell to the ground, covering their ears.

"Ah, don't like that do you?" he said putting the sonic away, "You see, I just turned on your entire PA system and am using it to broadcast a high pitched sound that is painful to you Klandians. One that will keep going until I tell it to stop, and considering the things you've done, that's not going to happen for a long, long time. Now then, Pinkie Pie! Toby! I know you can hear me wherever you are! I'm in the main control room in the center of the ship. I want you two to come here right away! I would very much like to see both of you right now!"

Within a minute, both Pinkie and Toby came walking into the main room. Upon seeing the Doctor, Pinkie immediately rushed forward and pulled him into a tight embrace.

"I'm so happy to see you Doctor!" she exclaimed, "I don't like it here! Lets go somewhere fun!"

"Of course," the Doctor replied pulling himself out of Pinkie's grip, "But first we have to save the others."

"Yeah!" Toby said, "We have to save Alice remember?"

"Oh, right. Sorry."

"Not to worry," the Doctor said, "We just need to find the harvesting room."

"I was just there!" Pinkie said.

"Really?"

Pinkie nodded. "Those guys were about to put me into one of those tubes and take my estrogems, or whatever, but then you guys showed up!"

"Wow, looks we got here just in time Toby. Lead the way my dear Pinkie."

"Okie Doki Loki!" Pinkie said and led them out of the room. They walked through the twisting corridors of the ship for about a minute before reaching the harvesting room.

"My god," the Doctor said as he looked around, "They've taken so many…"

Toby rushed into the room, looking at the ponies in each tube for a few seconds before moving onto another one. Finally, he stopped in front of a tube holding a light purple pony with a white mane streaked with black.

"Alice!" he exclaimed happily, "Doctor, I found Alice!"

"Good man Toby," the Doctor said walking over to him, "Now we just need to free her and the others."

"How are we gonna do that?" Pinkie asked.

"Well, we need to disconnect them from those helmets."

"Easy peasy!" Pinkie said, "We just open up the tubes and pull them off."

"Not quite. The tubes are attached directly to their brains. Just pulling the helmets off could cause irreparable brain damage."

"Then how do we get them off?" Toby asked.

"Very carefully," the Doctor replied.

* * *

It took a couple of hours, but with the help of his sonic screwdriver, the Doctor was able to disconnect the helmets from all of the kidnapped ponies. The ponies all lay on the floor in the center of the room, still unconscious.

"Are they gonna be okay?" Toby asked, sitting by his sister.

"They're going to be just fine," the Doctor said, "They just need some time to recover from their ordeal. They should all wake up fairly soon."

Then as if on cue, a few of the ponies began to stir. Opening their eyes, they sat up and looked around.

"What's going on? Who are you?" one of them asked.

"Hello there!" the Doctor cheerily replied, "I'm the Doctor. This is Pinkie Pie and Toby. We're here to rescue you."

"What happened to all those creepy little guys?" another asked.

"The Klandians? No need to worry about them. It's all been taken care of."

As the Doctor spoke, the rest of ponies began to wake up.

"Oh my…" Alice said as she awoke, "What's going on?"

"Alice!" Toby exclaimed, hugging his sister, "I'm so happy you're okay!"

"Toby? What are you doing here? Do mom and dad know you're here?"

"I came here to save you with my new friends the Doctor and Pinkie Pie."

"Indeed we did," the Doctor said, "And now that everyone's awake, if you could all follow me, I'll take you back to homes."

* * *

Using the TARDIS, the Doctor was able to return every single pony back to their homes very quickly. As they returned to Ponyville, the Doctor sighed.

"Well, I do hope you had fun today Toby," he said turning to the young colt.

"Well, it was a little scary and kinda dangerous, but yeah! I had a lot of fun today!" Toby replied.

"Thank you for everything Doctor," Alice said, "It was very nice to meet you and Pinkie Pie."

"Of course," the Doctor replied.

"It was super awesome meeting you to!" Pinkie said happily.

"So what's going to happen to those guys who kidnapped us?" Alice asked.

The Doctor turned back to console, face blank. "That's something for me to worry about," he said. He turned back around, smiling. "Now then," he said, "You two had best get back home before ponies start to worry."

"Oh, yes. Of course. Good bye Doctor, Pinkie," Alice said.

"Yeah, bye!" Toby said smiling.

The two of them left the TARDIS, waving goodbye as they did.

"So what now?" Pinkie asked when they were finally alone.

"Now, I'm going to need you to stay here in Ponyville for just a little bit while I deal with the Klandian ship," the Doctor replied.

"What are you going to do?"

"Something that you don't need to know about."

Pinkie looked at the Doctor for a moment, then slowly nodded. "Alright then, I'll see you later," she said and left the TARDIS. The TARDIS whooshed away, then returned about a minute later. Pinkie walked back into TARDIS and looked at the Doctor.

"Hello again Pinkie," he said with a nod.

"Is everything okay now?" Pinkie asked.

"Very much so," the Doctor said with a smile, "Now then, where should we go next?"

* * *

Thanks for reading, and be sure to leave a nice review!


	4. Everyone Loves the Circus

I don't own My Little Pony or Doctor Who in any way, shape, or form.

* * *

Chapter 4 Everyone Loves The Circus

"Somewhere fun…" the Doctor muttered as he walked around the TARDIS's center console, pulling levers and pushing buttons, "That's what you said, right Pinkie? You want to go somewhere fun?"

Pinkie nodded. "Yep! Somewhere fun!"

"Well, there're plenty of fun places out in the universe. All sorts of vacation and party planets catering to any and all forms of fun and pleasure. But which one should we go to? Hmm…" The Doctor looked thoughtfully at the ground for a moment. "Ah ha! I've got it!" he said suddenly, "The carnival planet, Relakis!"

"Carnival planet?" Pinkie said, wide eyed.

The Doctor smiled and nodded his head. "The entire planet is one giant carnival, complete with games, rides, sideshows, and all sorts of foods that really shouldn't be deep fried, but are. It's amazing."

"Lets go! Lets go!" Pinkie said excitedly, "I love carnivals!"

"I thought you would," the Doctor smiled as he pushed buttons and pulled levers, "To Relakis!"

"Wait a minute Doctor," Pinkie suddenly said.

"Yes?" the Doctor replied, turning towards her.

"How do you know about planets here? You said that this universe was new for you."

"Ah, yes, well… About that. It's true that this universe is new to me, but at the same time, it's familiar. You see, when I first arrived, I thought that this place would be so vastly different, what with the multicolored talking ponies, that I didn't think I'd see anything recognizable. But seeing the Jallpurian hunter and the Klandians tells me that the planets Jallpis and Klanda exist here. And if they exist, then lots of other planets from my universe are bound to exist here too."

"Oh, I see," Pinkie said nodding, "Makes sense."

"Alright then," the Doctor said hitting a few more buttons, causing the TARDIS to begin whooshing and grinding, "Lets be on our way then."

The TARDIS came to a stop and the two ponies exited. As she stepped out, Pinkie stopped and looked around, eyes wide, mouth hanging open. "Wow…" she said, "It's so bright and flashy!"

"Well, it is a carnival," the Doctor said as he stepped up beside her. The Doctor looked around as well, taking in everything. There were several large, brightly colored tents everywhere. Around and between them were several smaller booths containing carnival food and carnival games. There were large Ferris wheels and roller coasters and other carnival rides spread about as well. As he looked around, the Doctor spotted a small yellow tent off by itself. As he glanced at it, he could see a red pony-like creature walk inside. "Now then," he said, paying no mind to the yellow tent, "What do you want to do first Pinkie?"

"Roller coaster!" Pinkie exclaimed, bouncing up and down.

"To the roller coaster then. Bonzai! No, that's not quite it either… Lets just go to the roller coaster."

* * *

The two ponies spent several hours going from ride to ride, watching the shows inside the tents, playing games and eating ridiculously unhealthy carnival food.

"Ah, this is amazing! I can't remember the last time I had this much fun," the Doctor said as they walked out of a tent, a large stuffed bear on his back.

"I know!" Pinkie said, skipping along beside him, "And this balloon hat that clown made for me is awesome!"

"It is a rather nice balloon hat. Although I still say that clown is up to no good."

"Oh come on Doctor, he was just a clown."

"A creepy clown."

As they walked, they passed by the yellow tent as a scaly blue creature walked in.

"Hmm, curious," the Doctor muttered, glancing at the tent.

"Something wrong?" Pinkie asked, looking at the Doctor.

"Its that tent there," he said, pointing.

"The yellow one?"

The Doctor nodded.

"What's wrong with it?"

"Well, since we arrived, I've seen several people go in."

"So? Whatever's in there must be super cool!"

"Possible, however that's not what's odd. What's odd is that none of them have come back out."

"Well, maybe whatever's in there is so cool that the people inside don't want to came back out."

"Again, possible, but unlikely. Look at the size of the tent. Compared to the other ones, it's tiny. Considering the average size of the performing areas within the other tents and the amount of people I saw go in, there's absolutely no way that tent could hold it all."

"But your TARDIS is super tiny and the inside is bigger then Ponyville."

"True, but that's not the case here."

"Why not?"

"Because the whole bigger on the inside technology of the TARDIS is exclusive to one race and race only. The Time Lords."

"So it's a Time Lord tent then."

"No, haven't you been listening? I just said that it wasn't. There is absolutely no way that tent is Time Lord."

"Well, why not?"

The Doctor sighed and looked away, a faraway look in his eyes. "Because they don't exist here."

Pinkie looked at the Doctor, silent, waiting for him to continue.

"I took a small detour while I was dealing with the Klandian ship," he said after a moment, "I wanted to check on a few planets from my universe. The Time Lord's planet, Gallifrey, was amongst them. Only here, that planet, and the Time Lords, never existed. So, you see why it can't possibly be the Time Lords Pinkie?"

Pinkie nodded. "Yeah, got it. But that still doesn't explain what's going on in there."

"No. No it doesn't. And I really do not like not knowing what's going on."

"We're gonna go investigate it, aren't we?"

"You catch on quick," the Doctor said with a smile, "Yes, we're gonna go check it out. But first, we need to drop our stuff off at the TARDIS before we go. Wouldn't want my bear or your hat to damaged in the inevitable conflict."

"Conflict? Aren't we just investigating a tent?"

"And here I thought you were catching on. Danger seems to follow me around Pinkie. No matter where I go, no matter what I do, there is always a conflict of some kind and I'm always at the center of it. I'm not saying that it's my fault, its just bad things always seem to happen around me, and I really wish that it would stop."

Pinkie looked at the ground, absorbing the Doctors words. "I see," she said after a moment, "Well, maybe I should just stay in the TARDIS then."

"Not a bad idea, but we don't know what's going on in there. I may need your help in there."

Pinkie sighed and shook her head. "Thought so."

* * *

With their items safely stored within the Doctors blue box, the two ponies made their way back through the carnival. Reaching the strange tent, the two stood in front, looking it over intently.

"Hmm… Looks like an ordinary tent," the Doctor said, "But it holds a sinister secret."

"And there's something fishy going on inside," Pinkie said.

"A whole oceans worth," the Doctor agreed and pulled out his sonic screwdriver. He waved the sonic around a bit then brought it close to his face. "Hmm… Interesting."

"What is it?"

"The sonic can't seem to pick up anything."

"What's that mean?"

"No idea, and you know how I feel about that."

Pinkie nodded, saying, "We're gonna have to go in then, aren't we?"

"Indeed," the Doctor replied with smile, "Forward march! Oh god, that's even worse the last the last one. Ugh, whatever."

They walked into the tent and stopped inside, looking around. The inside of the tent was very bare, the only thing that seemed to be inside being a large round metal disc on the floor.

"Well, not what I expecting," the Doctor said.

"What were you expecting?" Pinkie asked.

"Not sure. Definitely not this though."

"Well, what is this?"

The Doctor leaned down to look at the disc more closely and began to scan it with the sonic. "Well, it appears to large metal disc," he replied standing back up.

"That's it?"

"Like I said before, the sonic isn't picking up anything, and that really worries me."

There was sudden flash of light, blinding the two temporarily. Shaking it off, they looked around and found that they were no longer in the tent.

"Doctor, what just happened? Where are we?" Pinkie said as she looked around.

"No idea," he replied, looking around as well. The new place that they were now at looked to be a large room. The floor, walls, and ceiling were a sparkling white, with large bright lights hanging down. There was an open doorway in one wall that seemed to lead into a hallway. "Well, wherever we are," the Doctor said, "We aren't to find out much standing around here. Come along, we have much to explore. Tally ho!"

The two walked into the hallway, looking around, watching for anything or anyone suspicious.

"Tally ho… Gah, they just keep getting worse and worse," the Doctor muttered as they went.

"What are you doing?" Pinkie asked.

"What do you mean?"

"You keep saying stuff like 'tally ho' and 'forwards' and then mutter about it not being good."

"Oh, that. I'm trying to come up with a catchphrase, and nothing feels right."

"Why do you need a catchphrase?"

"Because I always have a catchphrase."

"Well, why not just use one of your old ones then?"

"It wouldn't feel right. Every new body gets anew catchphrase. And, now that I think about it, a new outfit as well, and this saddlebag doesn't count. I'm going to need to do something about that when we get back to the TARDIS."

Pinkie looked at the Doctor a little confusedly as they continued down the hallway. The hallway was empty, the walls bare of doors and windows. They continued forward in silence, the hallway stretching endlessly forward.

"What is with this place?" the Doctor said after a moment, "This hallway never ends!"

"I think I know why Doctor," Pinkie said, stopping.

"Oh? Whys that?" he asked, stopping as well.

"Look behind us."

The Doctor turned and stared at what was behind them, eyes wide, mouth hanging open

"What? How is that even…" the Doctor said, trying to contemplate what he was seeing. Just behind them, not more then a couple of feet away, was the doorway that they had come through. "That's impossible!" he said, "We walked away from that! For several minutes! There's no way it should be that close to us!"

"Something is seriously wrong here Doctor."

"Most definitely. If only I could figure out what it was." The Doctor walked back through the door and looked around the room. Seeing that nothing had changed, he walked back out and stood next to Pinkie. He glared down the hallway and pulled out the sonic. He pointed it down the hallway for a moment, looked at it, than put it away with a sigh.

"Nothing?" Pinkie asked.

"Nothing," he replied, "What is going on here? Nothing about this makes sense."

"But in a way, not making sense does make sense," said a new voice from behind them.

Turning, they saw a clown standing in the doorway, smiling at them. The clown's body was pony-like, in that it had four legs that ended in hooves. The clown's head was large and round, almost bulbous, with a rainbow colored Afro wig sitting atop it. He had no coat, it's pale blue skin exposed in the places not covered by the brightly colored clown suit he wore.

"Hey, you're the clown that gave me the balloon hat!" Pinkie exclaimed upon seeing him.

"Indeed I am," he replied cheerfully, "I see that you are not wearing it though. I thought you liked it."

"I do!" Pinkie said, "I really do like it. I just didn't want it to get damaged in the inevitable conflict."

"Conflict? What conflict?" the clown asked confused.

"The conflict that's inevitably gonna break out."

"And why would you think something like that is going to happen?"

"Because there's always conflict around the Doctor," she gestured to the Doctor as she spoke, "Or, that what he says at least."

The clown looked at the Doctor and nodded his head. "I remember you," he said, "You were glaring at the whole time I was making your friend her balloon hat."

"Because I didn't trust you," the Doctor replied, eyes narrowing, "And it seems I was right not to. You're involved in whatever it is that's going on here, aren't you?"

"But of course," the clown said with a slight bow.

"Tell me then, what is it you're doing?"

"Oh now where would be the fun in that? You're going to have to figure that out for yourself."

"Fine, have it your way," the Doctor said turning back towards the hallway, "First things first. This hallway."

"Ah, yes, the first of many mysteries," the clown said moving next to the Doctor, "The endless hallway. However does it work?"

"Well, it's rather obvious. We aren't actually moving when we walk forward."

"Very good, very good. Now why aren't you moving?"

The Doctor looked down the hallway, deep in thought. He turned to the clown and smiled. "It's the floor," he said, "When we move forward, it moves backwards, like a conveyer belt, and keeps us in place."

"Ding ding ding!" the clown exclaimed, "Exactly right! Now then if you'll follow me, the next mystery awaits!"

The clown walked down the hallway, humming to himself as he did. The Doctor and Pinkie looked at each other, shrugged their shoulders, and followed the clown down the hall, actually moving through it as they did.

They followed the clown for a short while before arriving in a new room that looked exactly like the first room they arrived in.

"Well now, this is curious," the clown said, looking around, "This is the room you first arrived in, but we walked away from it. How can this be?"

"It's not the same room," the Doctor said with a sigh, "It's just a room made to look like the first room."

"Ding ding ding!" the clown exclaimed, "Correct! You're good at this."

"This is all far to easy," the Doctor said, "Anyone can figure this stuff out. If this is the best you can do, then this fun house isn't going to be very fun for me."

"Fun house?" Pinkie asked, confused.

"Yes. This is a fun house. Isn't that right clown?"

"Indeed," the clown said smiling, "You figured that very quickly. Good job."

"It was rather obvious actually. The tent leading here, the clown guide, the 'mysteries'. This is just a fun house for tourists."

"Then, there's nothing bad going on here?" Pinkie asked.

"Nope."

"But what about the people who didn't come out?"

"Ah, yes. Why is that?" the Doctor asked, turning to face the clown.

"Whatever do you mean?" the clown said, sounding innocent.

"I saw people go into the tent, but not come out. Where are they?"

"Oh, there is no need to worry about them. They are perfectly fine. They've all made it through here and are back out in the carnival."

"But I never saw them leave the tent. Explain that."

"The exit of the fun house leads to a different tent in a different part of the carnival."

"I see. So there's nothing sinister or nefarious going on here?"

"Of course not Doctor!" the clown laughed, "This is the carnival planet Relakis! Our only goal here is to entertain."

"I see. Lead us to exit then, I would like to leave."

"To reach the exit, you must solve all of the mysteries. It is the rule."

The Doctor sighed and shook his head. "Lead on then."

* * *

It took roughly twenty minutes for the Doctor to solve the remaining mysteries of the fun house and reach the final room.

"This is it then?" the Doctor asked as they stepped into the room.

"Indeed it is," the clown replied with a smile, "Thank you for coming. We hope to see you again."

"Doubtful" the Doctor said, "Come along Pinkie. Lets get out of here."

"Okie Doki Loki!" Pinkie replied moving next to the Doctor, "Bye Mr. Clown! See you later!"

There was bright flash of light and the two found themselves inside of a tent much the yellow one. They walked outside and found themselves standing in front of another small yellow tent in a different area of the carnival.

"Seems that clown was telling the truth," the Doctor noted, "Oh well, come on Pinkie. Lets get back to the TARDIS."

It didn't take long for the two to reach he TARDIS, as the second tent's location was fairly close.

"That was a lot of fun Doctor!" Pinkie said as they stepped inside.

"If by 'fun', you mean 'a complete waste of time', then yes. It was loads of fun," the Doctor replied with a sigh.

"Oh, come on! It wasn't that bad. There wasn't a conflict or anything."

"I guess that's true. I'd gotten so used to conflicts erupting around me, I'd almost forgotten that sometimes they don't. Now then, I'll be right back. I need to find some clothes to wear."

The Doctor walked off into the TARDIS, going down one of it's many hallways. Pinkie wandered around the console for a few minutes, waiting for him to return. When he did, he stopped in the doorway, striking a dramatic pose.

"Well, what do you think?" he asked, smiling. The Doctor now wore a black silk vest over the front part of his body. A small gold chain ran from a small loop into a pocket where the top part of pocket watch poked out.

"A vest?" Pinkie said, sounding less then impressed.

"Yes, a vest. Well it's true that I have a rather large collection of clothes, only a very small portion of those clothes can be worn by a pony. And of that very limited selection, this vest seemed to be the best choice."

"If you say so."

"I do. Now then, new outfit, but no catchphrase. Oh well, it'll come in time. For right now, we have a lot more to see and do. Lets be on our way."

"Okie Doki Loki! Just, one thing before we go."

"Yes? What is it?"

"Earlier, you said that the TARDIS is Time Lord technology, right?"

"Yes. I did say that. Why?"

"Well, I was just wondering, how'd you get the TARDIS?"

The Doctor sighed and gestured to a row of chairs against one of the walls. "Have a seat Pinkie."

"Um, ok," Pinkie said sitting in one of the chairs.

The Doctor walked over and sat down next to her. He stared silently at the ground for a moment before looking at her. "I'm going tell you a story Pinkie Pie, about a planet called Gallifrey, and a Time Lord called the Doctor."

* * *

Thanks for reading and be sure to leave a nice review!


	5. The Invasion of the Cyberponies

I don't own My Little Pony or Doctor Who in any way, shape, or form.

* * *

Chapter 5 The Invasion of the Cyberponies

"Whew, didn't quite go how I expected," the Doctor said as he entered the TARDIS, "But it all worked out in the end. And, it was all rather fun, eh?"

"Yeah, sure, fun," Pinkie grumbled, "I especially loved the part where I almost got thrown into a volcano."

"Yes, well, that was because the natives thought it would appease their god and end the drought."

"Why are you defending them?"

"I'm not defending them! I'm just telling you why they did what they did. I find that knowing why things happen make me feel a little better."

"I guess I do feel a little better."

"See? What'd I tell you? Now then, onto our next destination. What do you say we go somewhere on Earth? We've been spending a lot of time on other planets, and I'd really like to see more ponies."

"We should go to Canterlot then!" Pinkie said bouncing up and down.

"Canterlot?"

"It's the capital of Equestria. It's super fancy there and the princess lives there. You'd love it!"

"Princess?"

"Princess Celestia! She rules all of Equestria."

"Wouldn't that make her a queen?" the Doctor asked confused.

Pinkie shook her head. "Nope. She's a princess."

"Is there a queen then?"

"Nope."

"King?"

"Nope. Just the princess."

"Hmm, what an odd system. I'd like to meet this princess. To Canterlot!"

With a few quick button presses, the TRADIS whooshed away. When it stopped, the two ponies stepped outside and looked around. They found themselves standing in a large medieval looking city.

"This doesn't look like Canterlot," Pinkie said.

"I'm pretty sure it is," the Doctor replied. Pulling the pocket watch from his vest pocket, he opened it and looked at it intently. "Yes, this is definitely Canterlot, only were about five hundred years in the past from when we first left."

"Five hundred years?" Pinkie exclaimed incredulously.

"Yes, I know," the Doctor replied, putting the pocket watch away, "I'm going to have to recalibrate the TARDIS later. For now, I say we take a look around. There's bound to be all sorts of interesting things to see."

"Why not?" Pinkie said with a shrug, "We might even get to see the princess!"

"You mean Celestia?"

"Yep!" Pinkie said with a nod.

"But I thought she was the princess in your time."

"Celestia's been ruling Equestria for over a thousand years Doctor!"

"Wow, and I thought I was long lived," the Doctor said smirking, "Come along then. We have a princess to see. Andale! No, still not it."

The town was strangely empty. There were very few ponies outside as they walked around, and few they saw were all wearing very dirty, torn cloaks. When they saw the Doctor and Pinkie, the ponies they passed would turn away and look at the ground.

"Why are they doing that?" Pinkie whispered.

"Not sure. Maybe they think we're nobles. But I think there's something else we should be concerned with," the Doctor whispered back.

"What is it?"

"There are hardly any ponies out. A big city like this should have tons of ponies out and about."

"Maybe somepony at the castle will know what's going on," Pinkie said pointing.

The Doctor looked to where she was pointing and saw a large castle come into view. "Good idea," he said, "The princess will probably have answers."

They reached the castle quickly and stopped in front of the gate. "This is odd," the Doctor said, "Why aren't there any guards?"

"Lets ask the princess," Pinkie said.

They walked inside and looked around. The inside of the castle was, just like the city outside, strangely empty. The two ponies walked forward slowly and quietly, not wanting to attract attention.

"This is weird Doctor," Pinkie whispered.

"Yes, something is definitely wrong here," the Doctor agreed, "We need to find the princess and fast."

"No problem," Pinkie said with a smile, "The throne room is this way. Follow me."

Following Pinkie through the winding hallways of the castle, they soon found themselves in front of a large set of double doors.

"This is it then?" the Doctor asked, looking up at the doors.

"Yep!" Pinkie replied with a nod.

"I take it you've been here before."

Pinkie nodded again. "I know the princess personally."

"My, my. That is impressive. Now then, shall we?"

Pinkie nodded and the Doctor pushed the doors open. The walked into the throne room and found that it was filled with ponies wearing armor, all looking to the throne where a large white alicorn sat, speaking to them.

"And so, in conclusion," Celestia said, "We need to increase patrols around the city and… Who's there?" she suddenly called out, looking to the now open doors. All of the guards turned to face the Doctor and Pinkie as they stepped into the room.

"Oh, um hello there!" the Doctor said with a smile, "I'm the Doctor, and this is-"

"Doctor?" Celestia interrupted.

"Uh, yes," he replied, a little unsure.

"Arrest them!" she called out.

* * *

"Well, that did not go how I thought it would," the Doctor said.

"I know," Pinkie said with a sigh, "I didn't even know Canterlot had dungeons."

The two ponies sat in a cell below the castle. The cell was barely furnished; a bit of straw spread about on the ground in one corner, a plank of wood attached to the wall by chains with a torn sheet lying across it.

"It's a castle, of course it has dungeons. I just wish they hadn't taken my saddlebag. I would have been able get us out of here with my sonic, no problem."

"Why did the princess arrest us anyway? I'm her friend and you haven't even met her."

"Well, actually, we're five hundred years in the past, remember? You haven't been born yet. And as for me, based on the way she reacted to my name, it would seem that we have met. Or, will meet, in my case."

"Because your time lines go in different directions. Just because she knows you doesn't mean you know her."

"Yes, that's right. You really are brilliant. Anyway, sometime in the past, it seems I will meet the princess and do something that she really won't like and as a consequence, has a warrant for me to be arrested on sight."

"Well, can't you just, not do whatever you haven't done yet?"

"Unfortunately, no. The fact that we're sitting in this dungeon shows that I have done it. The event, whatever it may be, is a fixed point."

"A what?"

"A fixed point. An event in time that must always happen, no matter what. Trying to stop it or alter it in anyway will result in a massive paradox that could destroy the whole of reality."

"Oh. I see."

Just then, they heard a door open from somewhere outside their cell, followed by hoof steps coming towards them. When they stopped, they saw the princess standing in front of their cell, glaring at them.

"You have a lot of nerve showing your face around here after what you did Doctor," she said coldly, "This is a good trick however, changing your appearance like this. If you hadn't identified yourself, I wouldn't have recognized you."

"Changing my appearance? I don't know what you mean. I also do not what it is I have done to you, as I haven't actually done it yet."

"Stop playing dumb Doctor, it doesn't become you," she looked over to Pinkie and said, "And who is this? Some innocent filly you've tricked into following you around? Have you no shame Doctor?"

"No, it's not like that," Pinkie said, "I'm his friend. I chose to go with him."

Celestia looked at them silently for a moment before sighing. "I don't have time to deal with you right now Doctor. I have enough problems right now dealing with those strange armored ponies."

"What? What do you mean by that? What strange armored ponies?"

"Invaders from lands unknown. They come clad in armor covering every inch of their bodies with weapons unlike any we have ever seen, capturing my subjects and killing my soldiers."

"No. No, it can't be," the Doctor said, eyes wide.

"What is it Doctor? Do you know who these invaders are?" the princess demanded.

"I won't know for sure unless I see one, but it sounds like the Cybermen, or Cyberponies given the whole equine thing in this universe."

"What are Cyberponies?" Pinkie asked.

"If they're like the Cybermen, they were once a race of organic beings. They were a beautiful, brilliant race. They came up with an ingenious idea to prolong and improve their lives by upgrading themselves."

"Upgrading?" Celestia said, confused.

"It started small. Replacing failing organs and lost limbs with mechanical ones that wouldn't fail."

"I can see why they thought that was a good idea. Replacing ones frail mortal body with one that cannot die would certainly be an improvement."

"Yes, it seemed good at first, but it soon spun out of control. They soon began replacing entire bodies with mechanical ones. The only thing left of the original person was their brain, and that was for the sole purpose of powering the body. Those who were upgraded like this lost their emotions, becoming unfeeling machines with only one goal, to upgrade all life and kill anyone that resists."

"That's horrible!" Pinkie said.

"Would that mean that those who have been captured have been…?" the princess said.

"Yes princess. They've already been upgraded. There's nothing we can do for them now," the Doctor replied.

"No, that can't be! There has to be a way to help them!"

"The upgrading process destroys the original body. Even if we could extract their minds, there would be nowhere to put them."

Celestia looked away for a moment then sighed. "I may end up regretting this," she said turning back to them. Her horn glowed for a moment and the cell door made a small click and swung open.

"You're letting us go?" the Doctor asked surprised.

"You know a lot about these Cyberponies. I don't entirely like admitting this, but it seems that I may need your help in this matter."

"Oh, you'll most definitely need my help," the Doctor said, smirking as he left the cell, "And I can guarantee that you won't regret it. Now then, if I could have my saddlebag back, I can get to work."

* * *

Back in the throne room, the Doctor, Pinkie Pie, Celestia, and a soldier stood gathered around a table where a map of the city was laid out.

"Doctor, I would like you to meet the captain of the guard, Glimmer Blade," Celestia said, gesturing to the armor clad grey unicorn.

"Good to meet you Captain," the Doctor said with a nod.

"Wish I could say the same for you," Glimmer replied coldly, "From the things the princess has said about you, I don't think you should even be out of that cell."

"Hold your tongue Captain," Celestia snapped, "I don't like this either, but the Doctor is the only pony here who knows anything about the Cyberponies. We need his help in this."

"Fine then. I will work with him, but I won't like it."

"Fine by me," the Doctor said, "Now then, show me where it is the Cyberponies come in from."

"They come into the city from here," Glimmer said pointing to the map, "There is a forest just outside the city from there. We suspect they have a stronghold somewhere within."

"Quite likely. A thorough investigation is definitely needed."

"I'll gather a group of my best soldiers together and we will storm their stronghold."

"No, that would be a disaster. From what Princess Celestia has told me, you and your men are no match for the Cyberponies. I will not allow any more deaths on my watch."

"Then what do propose we do? We can not battle these invaders with just two ponies."

"There won't be two of us. Pinkie will be coming along as well."

"You want to bring a mare with us?"

"I wouldn't underestimate Pinkie I were you."

"Yeah!" Pinkie agreed, "I wouldn't underestimate me either."

Glimmer turned to Celestia with a look of concern. The princess sighed and shook her head. "If it is what the Doctor thinks is best, then it is what we shall do."

"Right! Now then, there's something I'm wondering Captain," the Doctor said, looking intently at the map.

"What's that?"

"When the Cyberponies attack, how large is their force?"

"Not very big. Four or five at the most."

"Just four or five? That can't be right… How long have the attacks been happening?"

"About a week now."

"So, for an entire week, four or five Cyberponies come into town, taking several ponies with them back to their base to upgrade them. By now, they should have small but respectable army."

"What's your point Doctor?" Glimmer asked confused.

"Well, it's just that an army of that size is more then enough to capture every single pony in town and wipe out all resistance. So why haven't they?"

"Are you suggesting that there's something else going on here?"

"I'm not sure. All I do know is that this isn't normal Cyberman behavior. It is possible that these invaders are not Cyberponies or that Cyberponies are not like the Cybermen of my universe. Either way, we need to find the stronghold and find out what going on."

"Right then," Glimmer said with a nod, "Lets go."

* * *

"This is it then?" the Doctor asked, standing at edge of town.

"That's right," Glimmer replied with a nod, "This is where they come from."

"Wow, it looks really creepy in there," Pinkie said a little shakily.

"Don't you worry Pinkie," the Doctor said smiling, "Just stick by me and everything will be fine."

"That's right," Glimmer said, "Stay behind us and we will protect you from all harm."

"Hey, I can take of myself," Pinkie said, "Not all mares are helpless you know."

"Like I said Captain," the Doctor said with a smug look, "I wouldn't underestimate Pinkie if I were you. Now then, enough standing around. Lets go on in. Charge! Huh… Not it either."

"What's he talking about?" Glimmer whispered to Pinkie as the entered the forest.

"Just ignore him," Pinkie whispered back.

"Lets see what we got here," the Doctor muttered to himself, ignoring the others, "If they came from this way, there should be signs of their movement through the forest."

"Like what?' Pinkie asked moving up next to him.

"Hoof prints, broken branches, areas of the grounds been worn down into something resembling a path, things like that."

"I don't see anything like that," Pinkie as she looked around.

"Look over there!" Glimmer exclaimed, pointing, "It looks like somepony cut a path through those bushes."

"Good eye Captain," the Doctor said walking over to the bushes, "Someone has definitely cut through here. And look at the ground, worn down as if several people had passed through this way frequently. This is the way they came."

"So if we follow this path, we'll find the base?" Glimmer asked.

"That's right," the Doctor nodded.

"Well, what are we waiting for? Lets go!" Pinkie said and rushed down the path.

"Pinkie wait! Slow down!" the Doctor called out after her. Growling, he turned to Glimmer Blade. "Come on Captain, we can't let her get to far ahead."

"Right," the unicorn agreed with a nod and the two colts set off down the path. The path winded through the forest for about a mile before a large metal structure came into view. Slowing as they approached it, the two colts could see Pinkie standing still, staring up at it.

"Doctor, look at it," she said as the two colts got close to her.

"Dear Celestia," Glimmer said under his breath, "Is that the stronghold?"

"Yes. That is, without a doubt, the Cyberpony base," the Doctor replied, "It really is them then."

"How are we going to get in there?" Glimmer asked.

"Through the front door."

"What? Won't they have guards stationed there?"

"Of course."

"They'll capture us if we go in that way then!"

"I know. That's the plan."

"You're plan is for us to get captured? That's insane!"

"Look, Glimmer," Pinkie whispered to the unicorn, "I know the Doctors plans seem crazy and don't make any sense, but they always work out. Trust me."

Glimmer sighed and shook his head. "Fine. You want us to get captured, we'll get captured."

"Glad you see it my way," the Doctor said with a smile, "Let's do it." Walking up to the front door, the Doctor placed his hooves against the door and gave it a firm push open. "Knock knock!" he called out as the doors swung open, then sighed, saying, "They just keep getting worse and worse."

The inside of the base was large and expansive. Large consoles and screens lined the walls and there several doorways leading down long hallways. In the center of the room stood a pony-like figure. The pony appeared to be made of shiny silver metal. Instead of a mane on it's head, two thin metal tubes came up from the side then bent at a ninety degree angle and met together at a small round node coming up from the top of the head. In place of its eyes were two round holes and in place of a mouth was a thin horizontal slit.

"Who are you?" it said with an emotionless mechanical voice as it turned to face them.

"I'm the Doctor and you, I'm guessing, are a Cyberpony?"

"That is affirmative. But I ask again, who are you?"

"I just told you. I'm the Doctor."

"Titles are meaningless," the Cyberpony said stepping forward in a slightly menacing manner, "What is your name?"

"The Doctor is my name."

"And who are the other two?"

"Pinkie Pie and Glimmer Blade," the Doctor replied gesturing to them.

"You are trespassing on a Cyberpony base. You will be deleted." The Cyberpony began to walk forward as it spoke, energy crackling around its front hooves.

"Wait, hold it!" the Doctor called out, "We're here to surrender ourselves to you! For upgrading!"

The Cyberpony hesitated, stopping just a few feet away from them, the energy around it hooves dying away. "Upgrading?" it said, a faint, almost unnoticeable hint of confusion in its voice.

"Yes, we heard that you were taking and upgrading the ponies around Canterlot and, well it sounded so wonderful, that we wanted to be upgraded as well."

"Upgrading is the ultimate fate of all life. You will follow me," the Cyberpony said, turning and walking towards one of the doorways.

"Doctor, I'm sure about this," Glimmer whispered as they followed.

"Don't worry Captain, its all part of my plan," the Doctor whispered back.

"Yeah, don't worry!" Pinkie whispered as well, "The Doctors plans always work out in the end."

Glimmer sighed and shook his head. "If you say so."

* * *

Thanks for reading, and be sure to leave a nice review!


	6. The Great Escape

I don't own My Little Pony or Doctor Who in any way, shape, or form.

* * *

Chapter 6 The Great Escape

The Cyberpony led the three ponies down a short hallway and into a large room. The walls of the room were lined with prison cells filled with ponies that looked like the peasants that they had seen around Canterlot.

"You will wait here," the Cyberpony said, ushering them into a cell.

"And how long will we be waiting?" the Doctor asked as the Cyberpony closed the cell door.

"Until we are ready."

"And that will be when?"

"When we are ready," the Cyberpony repeated and left the room.

"Well, we've been captured," Glimmer said sitting down, "What's the next part of your plan Doctor?"

"Next we gather information," the Doctor replied.

"From a prison cell? I don't think we'll be able to get much here."

"Oh you would be surprised," the Doctor said with a smile. Turning to one of the other ponies in the cell, the Doctor tapped him shoulder. "Hello there. I'm the Doctor," he said as the pony turned to him, "I was wondering if I could ask you a few questions."

"What is it you want to know sire?" the pony said, not looking at the Doctor directly.

"How long have you been held prisoner here?"

"About a week sire."

"And during that time, how many ponies have you seen the Cyberponies take out of here?"

"None sire."

"None? Are you sure?"

"I'm certain sire. Those armored ponies only ever bring ponies in here, never out."

"I see. Thank you."

"Of course sire."

Turning away, the Doctor moved back over to Pinkie and Glimmer. He sat down near them and stared at the ground, deep in thought.

"Well Doctor?" Glimmer asked, "Did you learn anything?"

"Something, but I'm not sure what it means."

"What is it?" Pinkie asked.

"It seems that the Cyberponies aren't taking their prisoners to be upgraded."

"That can't be right," Glimmer said, confused, "From what you said, their whole purpose in life is to upgrade others."

"Exactly," the Doctor said with a nod, "So why aren't they?"

"Maybe they can't," Pinkie suggested.

"But why can't they? That's what we need to find out next," the Doctor said.

"And how do you propose we do that?" Glimmer asked, "I don't think anypony here will be able to tell us."

"From a Cyberpony of course," the Doctor said as if it was incredibly obvious.

"I dunno Doctor," Pinkie said, "The Cyberponies don't seem to be very talkative."

"You just let me worry that, alright? I know how to make these guys talk."

Another Cyberpony came into the room at that moment, pulling a small cart with small containers sitting on it.

"Here is your daily sustenance," it said placing a container into each cell.

"Excuse me," the Doctor said when the Cyberpony came to their cell, "I was wondering, why haven't you upgraded anyone yet? Is there a problem with your machines or something?"

"Cease talking or you will be deleted," the Cyberpony said and left the room.

"Well, that could have gone better," the Doctor said after a moment.

"You can say that again," Glimmer grumbled.

"Now what?" Pinkie asked.

The Doctor stared at nothing for a moment then sighed. "Now, we wait."

* * *

The three ponies sat in silence for a couple hours before the Cyberpony returned, gathering the containers. When it reached their cell, the Doctor moved close to the bars, saying, "I can help you fix your machine."

The Cyberpony stopped and looked at the Doctor for a moment before saying, "Explain."

"I know a few things about your technology. Let me take a look at your machines and I can get them up and running again so that you can start upgrading everyone."

"You will wait here," the Cyberpony said and left.

"What are you doing," Glimmer said moving up next to the Doctor, "Why are you offering to help them?"

"It's a ploy Captain," the brown pony responded, "I get them to take me to their machine, improvise myself into an advantageous position and make them release everyone."

"You mean everypony," Pinkie said stepping up next to him.

"Sorry what?"

"Everypony," Pinkie repeated.

The Doctor stared at Pinkie with a look of disbelief for a few seconds then sighed and shook his head. "Of course that's what you say here," he said under his breath.

The Cyberpony from before reentered the room bringing a second, slightly larger Cyberpony with it. The second Cyberpony, in addition to being larger, looked a little different as well. Its head had a small, clear glass dome with several blinking lights.

"Well I'll be," the Doctor said, seeing the second Cyberpony, "It's a Cyber-Leader."

"A what?" Glimmer said.

"A Cyber-Leader. It's sort of a Cyberpony version of you. It's the one in charge of this little army."

"This is the one," the Cyberpony said gesturing to the Doctor as they approached the cell.

"You can fix our machine?" the Cyber-Leader asked.

"Indeed I can," the Doctor said with a smile.

"You will come with me," the Cyber-Leader said opening the cell.

"Right, yes, of course," the Doctor replied nodding, "I just have one condition."

"What is that?"

"Pinkie Pie and Glimmer Blade are to come with me."

"Why should we allow that?"

"They are my assistants and I will need their assistance in this."

The Cyber-Leader looked at the Doctor for a few seconds before looking to the other two ponies and saying, "You will follow me."

The three ponies followed the two Cyberponies out of the prison room and down another hallway into a large room. In the center of the room was a large machine that had several recesses that looked like they were made to hold a pony and multiple screens and control panels.

"What is that?" Pinkie whispered as they entered the room.

"The upgrading machine," the Doctor whispered back.

"You will fix the device," the Cyber-Leader said turning to the trio.

"Sure thing," the Doctor said, "I was just wondering though, how did the device get damaged?"

"We crash landed here," the Cyber-Leader replied.

"Crash landed?"

"That is affirmative. We crash landed on this planet and our device was damaged. You will fix it."

"Yes, okay! Just give me a minute! Gah, the Cybermen back home were never this pushy."

The Doctor walked up to the machine and began looking it over. As he walked back and forth before it, he pulled out his sonic screwdriver and started scanning it.

"Hmm, I think I see the problem," he said after a moment. Moving up closer to the machine, the Doctor ran the sonic over a small section, causing a small panel to open, exposing the inner workings. "Ah yes, just as I expected," he said looking at the exposed wires, "The conversion matrix has been completely destroyed. Pinkie Pie, you're going to need to go find another one."

"Okie Doki Loki!" Pinkie said, saluting the Doctor, "Just, um… Where do I get one of those?"

"Hmm? Oh, well, the Cyberponies probably have another one somewhere around here. Just go look around, you're bound to find one."

"Got it. Just, one more thing. What's a conversion thingy look like?"

The Doctor reached into the machine and pulled out a small grey box that was cracked in several places and look partially melted. "Like this, just, you know, less broken."

"Got it!" Pinkie said with a nod and rushed off.

"Follow her," the Cyber-Leader said to the other Cyberpony.

The other Cyberpony nodded and followed after Pinkie Pie.

"Okay Captain," the Doctor said to Glimmer, "I'm going to need you to go find twenty feet of wire, a box of fuses, a box of Jammy Dodgers, and a fez."

"What?" Glimmer responded, a very confused look on his face.

"Wire, fuses, Jammy Dodgers and a fez!" the Doctor repeated turning to him.

"I have no idea what any of that is," the unicorn replied shaking his head.

The Doctor sighed and looked to the Cyber-Leader. "I don't suppose you could get me twenty feet of wire and a box of fuses, could you?"

"Negative," the Cyber-Leader said, "Another will bring you the necessary components."

"Found one!" Pinkie sang as she came skipping back into the room, balancing a small grey box on her head.

"Oh, beautiful!" the Doctor said grabbing to box, "This is exactly what I needed." The Doctor ran the sonic over it for a few seconds, than placed it into the machine. "Alright good. Now I just need that wire and fuses."

"And then the machine will work?" the Cyber-Leader asked.

"Almost," the Doctor replied, "There's still something else, but I'm not sure what."

"You will fix it."

"Yes, I know. That's what I'm doing! You don't need to keep telling me!"

The Cyberpony that had followed Pinkie out of the room came back in carrying a large coil of wire and a small box.

"Ah, that's the wire and fuses I asked for then? Splendid," the Doctor said taking the items away from the Cyberpony.

"Affirmative," the Cyberpony said, "You will fix the device."

"Alright, if you all don't stop saying that, I'm not going to fix anything."

The Cyberponies looked at the Doctor in silence.

"Alright?" the Doctor asked, sounding a little nervous.

The Cyberponies continued to stare at him.

"Ok, right. Captain, I'm going to need you to measure out two three foot long lengths of wire," he said, handing the coil to Glimmer.

"Right," the unicorn replied and began measuring out the wire.

"Ok, now Pinkie Pie, you're going to need to replace all the blown fuses," the Doctor said turning to the pink mare.

"Okie Doki Loki! How will I know which ones are blown though?" Pinkie asked.

Reaching into the machine, the Doctor pulled out a fuse and held it up. "This is what a blown fuse looks like," he said, "So, just look for the fuses like this and replace them with these." As he said that, he picked up the box of fuses.

"Will do!" Pinkie said and began working.

"Here's the wire Doctor," Glimmer said handing him two short lengths of wire.

"Thank you Captain," he said taking the wire. The Doctor ran the sonic over the two wires then turned to Pinkie, saying, "Pinkie, after you're done with the fuses, I need you to attach these wires to the conversion matrix."

"How do I do that?" she asked taking the wire.

"There are two small openings on top of the matrix. The wires should fit in there."

"Got it," she said, attaching the wires, "Now what?"

"Now, I'm going to need you to step aside so I can do some tinkering."

Stepping up to the machine, the Doctor began rummaging around inside, detaching and reattaching wires and moving things around while muttering to himself.

"Can we really trust the Doctors plan?" Glimmer whispered to Pinkie as the Doctor worked.

"Of course!" Pinkie whispered back, "The Doctors plans always work out!"

"Right, well, I'm just not seeing how this plan is supposed to end."

"I never know how his plans are gonna work out, but they always do. So, just trust him, okay?"

"If you've got time to mutter Captain, you've got time to measure out ten feet of wire," the Doctor called out, still tinkering with the machine.

"Uh, right," Glimmer said, picking the wire back up.

"And I'm still waiting on those Jammy Dodgers!"

"Here you go Doctor," Glimmer said moving over to him with the wire.

The Doctor took the wire without a word and attached it to something inside the machine. Moving back, he closed the panel and ran the sonic over it.

"There we go," he said, turning to the Cyberponies, "All done."

"The machine is fixed?" the Cyber-Leader asked.

"In a way," the Doctor responded.

"What do you mean?"

"What I mean is this." The Doctor raised the sonic into the air and turned it on. Almost immediately, a loud klaxon began to blare throughout the base and red lights began to flash.

"Self-destruct initiated," a Cyberpony voice said from the PA system, "Base will destruct in three minutes."

"What did you do?" the Cyber-Leader said.

"I rewired your machine so that it would connect to your main systems. From there, it was child's play to use my sonic to set off your self-destruct sequence. And don't think you can just go turn it off. I'm the only one who can do that."

"You will stop the self-destruct."

"I could do that. Or I could just let this base explode."

"Then you will die with us."

"Actually no. You see, Pinkie Pie, Glimmer Blade and I will be leaving here quite soon along with all the other ponies you've captured."

"Base will destruct in two minutes," the PA announced.

"Times running out," the Doctor said, "So, go ahead and release the prisoners."

"We will not," the Cyber-Leader said, "You will be deleted."

The Cyber-Leader and the other Cyberpony began advancing on the Doctor.

"Oh no you don't!" the Doctor shouted and pointed the sonic at them. The Cyberponies stopped and stumbled back slightly. "Pinkie Pie, Captain, go! Get the others out of here, fast! I'll hold the Cyberponies off. But you have to act quickly!"

"Got it!" Pinkie said with a nod and rushed out of the room.

"Just be sure to follow us out," Glimmer called as he ran after Pinkie.

"Don't worry about me Captain," the Doctor called after him, "I know how to take care of myself."

* * *

Pinkie and Glimmer ran as fast they could back to the prison room. As they made their way into the main room of the base, two Cyberponies came into the room.

"Halt or you will be deleted," they called out.

"We don't have time for this," Glimmer growled, "Pinkie Pie keep going. I'll hold these two off."

"But Glimmer, we have to-"

"Go!" he interrupted, "I said before that I would protect you, and as a member of the Royal Guard, I am honor bound to keep my promises."

Pinkie looked at him for a second then nodded and ran off.

"Alright you metal freaks," Glimmer growled, his horn glowing, "Let's see what you've got."

* * *

Entering the prison room, Pinkie found a key lying on a small box near the door.

"Base will destruct in one minute," the PA called out.

"Gotta be fast," Pinkie mumbled picking up the key. She quickly ran around the room, opening all the cells. When the doors opened, the ponies all began rushing out of the room. After opening the last cell, Pinkie followed them out.

Back in the main room, the prisoners all ran to the main doors and pushed them open, rushing outside. In the center of the room, Glimmer stood, a sword made of a glowing light floating in front of him, slashing at the Cyberponies, keeping them away.

"Glimmer, I got the prisoners out!" she called to him, "We need to get out of here!"

"You go on ahead!" he called back, "I'll be out soon!"

Pinkie nodded and rushed outside as PA called out, "Base will destruct in thirty seconds."

Reaching the outside, Pinkie ran into the forest, trying to follow the path they had taken earlier, then stopped and turned around. She could just barely see the Cyberpony base in the distance from where she had stopped. Just then, Glimmer Blade came running towards her.

"Pinkie Pie!" he called out upon seeing her, "Where's the Doctor? Did he make it out?"

"I didn't see him," she replied shaking her head, "I think he's still in there."

Suddenly, there was a loud explosion and a large ball of fire shot up into the sky.

"NO!" Pinkie screamed as the Cyberpony base exploded, "DOCTOR!"

She tried to run back towards the base, but was held back by Glimmer Blade.

"Pinkie stop it," he said, "There's nothing we can do!"

"But, the Doctor… He… He…"

"He gave his life so that we could escape and get the others to safety. He was a valiant and honorable pony. Let's not waste his sacrifice by running back into the flames. We need to get the captured ponies back to Canterlot."

Pinkie just stared at the burning wreckage of the Cyberpony base, unable to speak.

"Pinkie please, we need to go."

Pinkie looked at Glimmer, her eyes blank, then turned around and walked back towards Canterlot.

* * *

"I see," Princess Celestia said, looking at the ground, "I may not have fully liked him, but the Doctor was a brave and honorable pony. His sacrifice will not be forgotten. I just wish I could have thanked him in person for his deeds today."

Glimmer Blade and Pinkie Pie had made it back to Canterlot with the rest of the ponies safely and were now sitting in the throne room. Glimmer had recanted the day's events to her while Pinkie just sat there looking at the ground, her face a blank mask.

Glimmer nodded, his expression grave. "I feel much the same way Princess. He saved all of Equestria this day. I do not know what it was he did in the past, but I do believe this makes up for it."

"Perhaps you're right Captain. Perhaps it is time I forgave him."

"Good to hear," a new voice called out from the doorway, "Now if I only knew what it was I did…"

Pinkie perked up at the sound of the voice and turned around, eyes growing large and her expression brightening. "Doctor!" she called out and rushed towards the brown pony, pulling him into a tight embrace, "Doctor I was so worried!"

The Doctor embraced Pinkie as well, saying, "I'm sorry I worried you Pinkie Pie. I'll try not to in the future."

"Doctor, I… I don't know what to say," Celestia said, looking very surprised.

"How did you escape?" Glimmer asked.

"Ah, yes, how I got out," the Doctor said, pulling himself out of Pinkie's hug, "It was a very narrow escape, very touch and go near the end."

"So how'd you get out?" Pinkie asked.

"Well, when you two ran off to save the prisoners, and I was holding of the Cyberponies, I found a frequency on the sonic that disrupted their movement, which bought me a few precious seconds that I used to download the blueprints of their base into my sonic," the Doctor explained, looking somewhat smug, "Using it as a map, I ran for a back exit, leading the Cyberponies deeper into the base. I found the exit just in time to get out before everything went all explodey. The Cyberponies weren't so lucky…"

"You mean they…" Celestia began, than stopped when the Doctor nodded his head.

"I didn't want it to end like that," he said, looking away from them, "I tried to reason with them as I was leading them away, but they wouldn't listen." The Doctor sighed and shook his head. "I guess some things are the same no matter where you go."

"That matters not Doctor," Celestia said, "You have saved all of Equestria and shown me your true nature. I was wrong in my earlier judgments of you."

"I'm sorry too Doctor," Glimmer said, "I based my feelings about you on hearsay and second hoof accounts. I should have waited until I had actually met you to form my opinions."

"Oh, no harm done," the Doctor said, waving a hoof dismissively, "It's all water under the bridge now. Don't worry yourselves about it."

"What will you do now Doctor?" Celestia asked.

"I don't know. What are we going to do next Pinkie?" the Doctor asked, smiling.

"Hmm, I don't know either Doctor," the pink mare said, smiling as well.

Celestia laughed and nodded her head. "I see, I see. Well, I wish you luck in your travels Doctor."

"Thank you princess," the Doctor said with a bow, "Until we meet again." He turned to Glimmer Blade and saluted him. "Farewell to as well Captain. Best of luck in your duties."

"You to Doctor," he replied with a salute of his own, "And to you Miss Pinkie Pie."

"Yeah?"

"Keep him out of trouble."

"Will do!" Pinkie said saluting him.

"Oi! I'm right here you know!" the Doctor interjected and everypony burst into laughter.

* * *

Back on the TARDIS, the Doctor walked around the console, pulling levers and pushing buttons. Pinkie sat on a nearby chair, smiling. "So, how'd you like Canterlot?" she asked.

"It was a nice city. Probably would have enjoyed it more without the Cyberponies though," he replied.

"It's not normally like that."

"I would hope not. Probably gonna have to end up going back there sometime. Now then," he said stepping away from the console, "Earlier today Pinkie, you called me your friend."

"Course I did!" she said nodding, "I mean, I may not have known you as long as the others back in Ponyville, but you're definitely my friend."

The Doctor smiled and nodded his head. "I feel much the same way. That being said, there's something I want to give you. Close your eyes and hold out your hoof."

"Okie Doki Loki!" Pinkie said, eyes shut tight, hoof extended. She felt the Doctor place something in her hoof, than heard him say, "Alright, you can open your eyes now."

Opening her eyes, Pinkie saw a small gold key in her hoof. She brought it closer to her face and looked it rather intently. "A key?" she asked, a little confused.

"Not just any key," the Doctor replied, "It's a key to the TARDIS. As long as you have that key, you will always be able to enter, even if I'm not with you."

Pinkie's eyes widened as the Doctor spoke. She looked up at him, mouth open, trying to speak, but found it difficult. After a moment she stammered, "R-really?"

The Doctor nodded. "Really."

Pinkie smiled and pulled the Doctor into a tight embrace, saying "Thank you, thank you, thank you."

"Your welcome Pinkie. Your welcome."

* * *

Thank you for reading and be sure to leave a nice review.


	7. What Lies Below

I do not own My Little Pony or Doctor Who in any way, shape, or form.

* * *

Chapter 7 What Lies Below

"And here we are," the Doctor said as the TARDIS stopped, "Ponyville, just after we left."

"Awesome!" Pinkie Pie said, skipping out of the doors, "It's good to be home! I bet my friends will be so happy to see me after I've been gone for so long!"

"Pinkie Pie, I landed us here ten minutes after we left. Your friends don't even know you were gone," the Doctor said walking up next to her.

"But we've been gone for like a month!"

"Time machine remember? I can bring us to anyplace at anytime."

"Oh yeah. So we're ten minutes from when we first left?"

"Yep," the Doctor said pulling out his pocket watch, "Ten minutes… ish."

"What do you mean 'ten minutesish'?" Pinkie said turning to him.

"Well, we certainly did arrive ten minutes after we left, plus an additional fifty."

"Wait a second… Ten minutes plus fifty minutes is…" Pinkie looked at the ground for a moment then looked up at the Doctor with wide eyes, "We're here an hour later?"

"Yes, well… This is a new universe for me! I'm still getting used to the timing here. And I'm still not entirely used to these hooves. Besides, look on the bright side. It's still the same day."

"True. And I guess it's not that bad."

"Oh? Why's that?"

"Well, everyday I take an hour out of my schedule for some time to myself."

"Ah, so we left during that alone time then?"

"Yep! So just as long as nopony came looking for me, everything should be fine."

The Doctor nodded his and began walking forwards. "Well, now that we're here, I do believe you owe me a proper tour of the town."

"Can do!" Pinkie said with a big smile and followed the Doctor forward.

"Hmm, looks a lot like it did in the future," the Doctor observed.

"Yeah, it's pretty much the same," Pinkie nodded, "There are a few things that are different though. Come on, this way!"

"Pinkie Pie! There you are!" called out a voice from above.

"Huh? Who's that?" the Doctor said looking around.

"Oh, it's Rainbow Dash!" Pinkie said looking up and waving a hoof, "Hi Dashie!"

A light blue pegasus descended and landed next to them. Brushing back a bit of her rainbow mane from her face, she smiled and said, "I've been looking all over for you. Where were you?"

"Hmm? Oh, uh, I was just showing my new friend around," the pink mare said pointing to the Doctor.

"Hello there," he said holding out a hoof, "I'm the Doctor. Nice to meet you."

"Rainbow Dash," the pegasus replied shaking his hoof, "I don't think I've seen you around before. You new in town?"

"Uh, yeah. Something like that. I take it you're a friend of Pinkie Pie?"

"Yep!" Pinkie said pulling Dash into an unexpected hug, "Dashie is my bestest friend in the whole world!"

"Ah, well, any friend of Pinkie's is sure to be a friend of mine."

"Uh, yeah sure," Dash said pulling herself away from Pinkie, "Just, uh, one question."

"What's that?"

"Doctor who exactly?"

"It's just the Doctor."

Rainbow Dash looked at him for a moment and shrugged. "If you say so. Anyway, I need to talk to you Pinkie."

"Sure thing Dashie! What's up?"

"Well, I got this great idea for some pranks involving a bucket of syrup and I figured you could probably get some form Sugarcube Corner."

"I don't know… Mr. and Mrs. Cake might not be too willing to give me that much syrup. Especially not after that prank we did with the frosting."

"Darn," Dash muttered, "I really looking forward to this prank."

"Um, excuse me Spectral Blitz, I think I can help you," the Doctor said, stepping forward slightly.

"My name's Rainbow Dash."

"Yes whatever. I'm fairly certain I have a very large quantity of maple syrup in my kitchen. I could go get you a few bucketfuls."

"Really? You'd do that for me? A complete stranger?"

"Like I said Prismatic Runner, any Pinkie's is a friend of mine."

"Awesome!" Dash exclaimed, "And my names Rainbow Dash."

"Right, that. If you'll give me a few moments, I'll bring you all the syrup you'll ever need." Turning, the Doctor quickly rushed back towards the TARDIS.

"That guys kinda weird," Dash said as he ran off.

"Yeah, I guess so," Pinkie agreed with a shrug, "But he's also pretty cool."

"Not as cool as me!" Dash exclaimed.

"Nopony could ever be as cool as you Dashie," Pinkie laughed.

Suddenly, the ground shook. It was a very light shaking that only lasted a few seconds and was accompanied by a low, almost inaudible rumble.

"Whoa, did you feel that?" Dash said, glancing around.

"Yeah, I wonder what that was," Pinkie said looking around as well, "I don't see any smoke and there aren't any ponies running around… Wait, there's some birds flying away over there."

"Huh? What're you talking about?" Dash said trying to see what Pinkie was looking at.

"Sorry Dashie, but I gotta go," Pinkie said walking forward. She stopped after a couple of steps and turned back to the pegasus. "I'll, uh, see you later I guess," she said and then ran off.

"Uh, yeah… Later," Dash mumbled as she left.

* * *

Pinkie ran as fast as she could towards where she saw the birds flying away. As she did, she felt the ground shake again.

"Again?" she muttered to herself, "Can't be an earthquake then… I hope the Doctor knows what's going on."

Within a few seconds, she reached a clearing within a small area of trees where she found the Doctor looking around, muttering to himself. As she entered the clearing, the Doctor turned towards her and nodded.

"Hello Pinkie," he said, "Come to see what's going on eh?"

"Yeah," Pinkie said nodding, "Any idea what caused that rumbling?"

"No," he responded looking at the ground, "But it seems to have come from somewhere around here. It hasn't caused any damage though, which is quite strange."

"Whys that?"

"Whatever caused the rumbling is strong enough to shake the ground so hard that you were able to feel it all the back in Ponyville. And if it was able to shake the ground that hard, the ground should at least be cracked. And look at the trees around here. All still standing, no damage to them either. It doesn't make sense."

"Hardly anything we do makes sense."

"True, but at least those other times the things that didn't make sense didn't make sense in a way that made sense."

Pinkie nodded and said, "True. So, then way is this not making sense in a way that doesn't make sense?"

"A good question Pinkie, a very good question. We need to get back to the TARDIS. Maybe I can find some answers there."

The ground shook again, feeling stronger and lasting longer within the clearing.

"And I think we should get there quickly."

* * *

"Alright," the Doctor said as they neared the TARDIS, "Here we are. Why don't you do the honors Pinkie?"

"Sure thing!" Pinkie said bouncing happily up to the door. As she got up to it, Pinkie pulled her key out of seemingly nowhere and unlocked the door.

"Very good," the Doctor said stepping up and pulling the door open.

"Hey, what are you guys doing?" a voice suddenly called out from behind them.

Turning, the two saw Rainbow Dash floating low over the ground towards them.

"Oh, hi Dashie!" Pinkie said waving.

"How did you find us Chromatic Sprint?" the Doctor asked confused.

"It's Rainbow Dash, and I found you guys by following Pinkie," she replied, "So, what are you guys doing? What's that blue box thing?"

"Um, well, it's uh…" the Doctor stammered nervously.

"That's the TARDIS!" Pinkie said cheerfully, "We're gonna go in and try to find out what's making everything all rumbly!"

"I'm sorry, what?" Dash replied.

The Doctor sighed and placed a hoof against his forehead. "Maybe I should explain," he muttered, "As I said before, I'm the Doctor. I'm a time traveling alien from another dimension. This blue box behind me is the TARDIS, a machine capable of traveling through time and space. Pinkie and I are going to use the TARDIS's various computers and other technological whatnots to try and find out what is causing the various tremors you've no doubt felt."

Rainbow Dash looked back and forth between the two for a few seconds before saying, "This is some kind of prank right?"

"No way! This is serious Dashie!" Pinkie said shaking her head.

"Really? 'Cause it sounds pretty crazy, even for you Pinkie."

"Well, it's not, okay? Here, I can prove it! Come with me!" As she spoke, Pinkie grabbed Dashes hoof and pulled her into the TARDIS, the Doctor following close behind. "Well, what do you think?" Pinkie asked.

Rainbow Dash stood there for a moment, staring at everything, eyes wide, mouth hanging open. "Ah guh wuh buh…" she stammered. Clearing her throat, Dash composed herself somewhat and said, "The inside… It's bigger then the outside! How is that even possible?"

"Complicated sciencey reasons," the Doctor said walking past her, "But we don't have time for that. We have other things to look into right now."

"Right!" Pinkie said, "We need to find out why the ground keeps shaking!"

"Uh, well, yes I suppose, but what I was referring to was Miss Technicolor Rush here," the Doctor replied looking at Rainbow Dash.

"Huh? What about me? And the names Rainbow Dash!"

"Well, you're a pegasus right?"

"Yeah, so what?"

"Well, you're the first pegasus I've really seen close up. And looking at you, well, you're wings just don't seem right."

"What's wrong with my wings?"

"They're to small."

"To small? I'll have you know my wings are a perfectly normal size for a pegasus my age!" Dash snapped, sounding very defensive.

"That may be, but they still look like they're to small for you to be able to fly with."

"Yeah? Well I can fly, see?" she said floating up of the ground a few inches.

"But you shouldn't be able to! You're wings are far too small to lift a pony of your size and weight! It's physically impossible!"

"And yet I'm flying."

"But you…!" The Doctor shut his eyes tight and breathed deeply in through his nose. "Just calm down Doctor," he muttered to himself, "This isn't your universe. Things are different here. Just breathe, and calm down." Opening his eyes, he looked back to Rainbow Dash. "I'm sorry I snapped at you. I keep forgetting that things work differently here. If your wings let you fly, then they let you fly. I'll just chalk it up to the apparently magical nature of this world. Now then, enough of that. We have to other things to do."

"The rumblyness?" Pinkie asked.

"The rumblyness," the Doctor replied and walked over to the center console.

"Uh, sorry, what's going on again?" Dash asked.

"You've felt those tremors around town right?" he asked not looking away from the buttons and levers he was pulling and pushing.

"Yeah. They started about twenty minutes ago," she replied.

"Twenty minutes ago? That's after we left!" Pinkie exclaimed.

"Wait, what do you mean you left?" Dash asked.

"The Doctor showed up here about a month ago and we started traveling around the universe and going on adventures and stuff!" Pinkie replied.

"Wait, how can you have been gone for a month? You were here all last month!" Dash exclaimed.

"Time travel," the Doctor said without looking up, "While we have been traveling around for a month or so, only about an hour has passed here since we left."

The blue pegasus looked at the two of them then sighed and shook her head. "This is way to weird for me," she muttered.

"Right, well, if we've got that all out of the way, we still have the matter of the tremors to deal with," the Doctor said.

"Isn't it just earthquakes?" Dash asked.

The Doctor shook his head. "No, it's something else. The tremors are too frequent to just be earthquakes. Something's causing them. Something big. Something powerful. Something that I have no idea what it is."

"That sounds bad," Dash said.

"Very much so," the Doctor said turning around and walking back out of the TARDIS, "Fortunately, I now have a few vague ideas as to who or what it might be, and so I'm going to need to investigate the epicenter a little more closely to figure it out."

"Need any help Doctor?" Pinkie asked.

"If you two are willing," he replied pushing the doors open.

"Course we are!" Pinkie exclaimed grabbing Rainbow Dash and dragging her out with her.

"Wait! Hang on! I didn't agree to this!" Dash tried to protest but was ignored.

* * *

"Seriously Pinkie!" Dash yelled as they arrived back in the clearing, "Just leave me out of this!"

"No way!" Pinkie said, "You're involved, so you have to see it through to the end. That's one of the Doctors rules."

"The only reason I'm involved is because you dragged me into this! I just wanted to pour syrup on ponies heads!"

"Come on Dashie, it'll be fun!"

The pegasus sighed and grumbled, "Fine. But when this is done, don't bother for the rest of the day, okay?"

"If you two are done muttering over there, I'm about to do some clever things and would really appreciate it if you would stand around looking impressed," the Doctor called out over his shoulder.

"Okie Doki Loki!" Pinkie said skipping over to him.

"Uh, ok…" Dash said a little unsure and moved next to Pinkie.

"Now then, the TARDIS was able to pinpoint the source of the rumbling as some kind of large subterranean vehicle that is currently headed here, to this forest clearing."

"Is it mole ponies?" Pinkie asked.

"No, that's just silly," the Doctor replied, "It's most likely lizard ponies."

"Uh, hate to disagree with you, since you seem to be something somewhat resembling an expert on this stuff, but lizard ponies sounds way sillier than mole ponies," Rainbow Dash said with scoff.

"That's because you've never met Silurians."

"Sil-what now?"

"Silurians. Back where I came from, they were a race of reptilian humanoids that evolved from dinosaurs. They put themselves into hibernation in their underground cities to try and avoid what they believed to be a world ending event, and thus they slept for millions of years before they woke up to find that homo sapiens had become the dominant species," the Doctor explained

"Homo what nows?"

"Homo sapiens. Human beings. Have you not heard of them here?"

"Wait a minute, humans? Pinkie, aren't humans those things Lyra's always talking about?" Dash asked.

"I think so," Pinkie replied, "But I thought they were just some kind of made up fairy tale creature."

"Oh they are very real. Where I come at least. I kind of used to be one."

"Man, Lyra would love to met you."

"I'm sure she would. Now then, back to the issue at hoof here. If it really is the Silurians coming up here, they'll be coming with the goal of total global conquest in mind."

"What's that mean?" Pinkie asked.

"They're going to try and take over the planet."

"Oh. That's bad."

"Quite. But don't worry. I've dealt with them many times in the past. No matter what happens, no matter what they try, I will fight them. And I will not stop fighting until I have completely stopped them from conquering this world, because I am the Doctor. And I am this planets protector."

"Since when?"

"Since I first arrived here. Now, enough questions. They're going to be here soon."

At that exact moment, the ground began to shake, harder and longer then before. As the ground shook, trees began to tilt and fall and large cracks formed across the clearing.

"Well, speak of the devil," the Doctor muttered, "Alright, we need to move back now!"

The three ponies moved back as the ground began to bulge and a large spinning drill erupted from the center of the clearing, followed by a large cylindrical vehicle. A hatch on the side opened and two strange pony-like figures exited.

The Doctor stared at them for a moment, before saying, "It seems I'm wrong."

"What do you mean?" Dash asked.

"Those are not Silurians."

"Then what are they?" Pinkie asked.

"No idea," he replied and began to move towards them, "Hello there! I have no idea who or what you are. Could you please tell me?"

The pony-like creatures turned to look at the Doctor. Their bodies were roughly the size of an average pony and had dark and very fuzzy coats with no manes or tails. Their heads looked slightly off, the muzzles looking far to shortened and rounded and they had a pair of long rodent-like buckteeth extending out of their mouths. Their eyes were solid black and squinted, as if the light was hurting them.

"We are mole ponies," one of them said in a low raspy voice, "My name is Digger and this is Burrow."

"Doesn't seem so silly now, does it?" Pinkie said smugly.

The Doctor shot Pinkie a small glare, than turned back to the mole ponies. "Nice to meet you," he said, "I'm the Doctor. Is something you want here?"

"We came for the Jallpurian," Burrow replied, "Where is it?"

"I believe I sent it to Skapatil Prime."

"Wait, what?" Digger said, confused, "You sent it somewhere?"

"Yes. It was on the verge of devouring an entire town, so Pinkie Pie," the Doctor gestured towards the pink mare, "And myself took charge and dealt with it."

"Ah, dammit," Burrow muttered and kicked the side of the drilling vehicle, "Beaten to the punch. Again."

"What do you mean again?" Dash asked.

"A few years ago we came up to the surface to capture a Serpaxian but it was already gone by the time we got here," Digger explained, sitting down, "About a year later, same thing happens again, with an Uplagit scout. And now this."

"We are the worst alien hunters ever!" Burrow yelled, kicking the vehicle again.

"Alien hunters?" the Doctor asked confused.

"Yeah," Digger said nodding, "Whenever aliens show up on this planet, we come up to the surface to try and catch them."

"I see. And are you doing this for any particular reason?"

"We need an army to combat the Light," Burrow responded.

"What's the Light?" Pinkie asked.

"The death of everything," Digger replied. The two mole ponies then, before anyone else could speak, climbed back into their drill vehicle and proceeded to head back underground.

The three ponies stood there for a moment staring at the giant hole in the ground. The Doctor then turned and began to walk away, saying, "Rainbow Dash, Pinkie Pie, come along. We have a lot of work to do."

* * *

Thanks for reading and be sure to leave a nice review!


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